[med-svn] r13283 - in trunk/packages/soap/soapdenovo2/trunk/debian: . patches

Olivier Sallou osallou at alioth.debian.org
Wed Apr 10 15:17:22 UTC 2013 

Author: osallou
Date: 2013-04-10 15:17:22 +0000 (Wed, 10 Apr 2013)
New Revision: 13283

Removed:
   trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_gcc_path
Modified:
   trunk/packages/soap/soapdenovo2/trunk/debian/changelog
   trunk/packages/soap/soapdenovo2/trunk/debian/control
   trunk/packages/soap/soapdenovo2/trunk/debian/copyright
   trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening
   trunk/packages/soap/soapdenovo2/trunk/debian/patches/series
   trunk/packages/soap/soapdenovo2/trunk/debian/watch
Log:
remove .a files from upstream archive and updates patches

Modified: trunk/packages/soap/soapdenovo2/trunk/debian/changelog
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/changelog	2013-04-09 17:54:02 UTC (rev 13282)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/changelog	2013-04-10 15:17:22 UTC (rev 13283)
@@ -1,4 +1,4 @@
-soapdenovo2 (223-2) unstable; urgency=low
+soapdenovo2 (223+dfsg-2) unstable; urgency=low
 
   * debian/copyright: Update copyright years and content
 

Modified: trunk/packages/soap/soapdenovo2/trunk/debian/control
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/control	2013-04-09 17:54:02 UTC (rev 13282)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/control	2013-04-10 15:17:22 UTC (rev 13283)
@@ -1,7 +1,7 @@
 Source: soapdenovo2
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 8), hardening-includes, zlib1g-dev
+Build-Depends: debhelper (>= 8), hardening-includes, zlib1g-dev, libbam-dev, libaio-dev
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Olivier Sallou <osallou at debian.org>
 DM-Upload-Allowed: yes

Modified: trunk/packages/soap/soapdenovo2/trunk/debian/copyright
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/copyright	2013-04-09 17:54:02 UTC (rev 13282)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/copyright	2013-04-10 15:17:22 UTC (rev 13283)
@@ -1,6 +1,9 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: soapdenovo
 Source: http://soap.genomics.org.cn/soapdenovo.html
+Files-Excluded:
+    standardPregraph/*.a
+    sparsePregraph/*.a
 
 Files: standardPregraph/inc/bam.h standardPregraph/inc/faidx.h sparsePregraph/inc/bam.h sparsePregraph/inc/faidx.h
 Copyright: 2008 Genome Research Ltd (GRL)

Modified: trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening	2013-04-09 17:54:02 UTC (rev 13282)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening	2013-04-10 15:17:22 UTC (rev 13283)
@@ -7,9 +7,9 @@
 --- a/standardPregraph/Makefile
 +++ b/standardPregraph/Makefile
 @@ -8,7 +8,11 @@
- CC=             gcc #gcc
- GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4)
- GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4)
+ CC=             gcc
+ #GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4)
+ #GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4)
 -CFLAGS=         -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
 +CFLAGS=        -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
 +CFLAGS += `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS`
@@ -19,7 +19,7 @@
  DFLAGS=         
  OBJS=		arc.o attachPEinfo.o bubble.o check.o compactEdge.o \
  		concatenateEdge.o connect.o contig.o cutTipPreGraph.o cutTip_graph.o \
-@@ -81,7 +85,7 @@
+@@ -83,7 +87,7 @@
  
  SOAPdenovo:	envTest $(OBJS)
  		@printf "Linking...                                                \r"

Deleted: trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_gcc_path
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_gcc_path	2013-04-09 17:54:02 UTC (rev 13282)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_gcc_path	2013-04-10 15:17:22 UTC (rev 13283)
@@ -1,41 +0,0 @@
-Subject: gcc wrong hard coded path
-Description: remove path for gcc
-Forwarded: yes
-Author: Olivier Sallou <osallou at debian.org>
-Last-Updated: 2013-02-09
---- a/sparsePregraph/Makefile
-+++ b/sparsePregraph/Makefile
-@@ -1,11 +1,11 @@
--CC=             /opt/blc/gcc-4.5.0/bin/gcc #gcc
-+CC=             gcc #gcc
- CFLAGS=         -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
- DFLAGS=         
- OBJS=		build_graph.o build_edge.o multi_threads.o \
- 			build_preArc.o pregraph_sparse.o io_func.o\
- 			global.o convert_soapdenovo.o
- PROG=           
--INCLUDES=	-I./inc
-+INCLUDES=	 -I./inc
- SUBDIRS=    . 
- LIBPATH=	-L/usr/lib64
- LIBS=       -pthread -lz -lstdc++ -L./inc
---- a/standardPregraph/Makefile
-+++ b/standardPregraph/Makefile
-@@ -5,7 +5,7 @@
- #
- ###################################
- 
--CC=             /opt/blc/gcc-4.5.0/bin/gcc #gcc
-+CC=             gcc #gcc
- GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4)
- GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4)
- CFLAGS=         -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
-@@ -78,8 +78,6 @@
- 
- envTest:
- 		@test $(BIT_ERR) != 1 || sh -c 'echo "Fatal: 64bit CPU and Operating System required!";false;'
--		@test $(GCCVERSIONMAJOR) == 1 || sh -c 'echo "GCC version lower than 4.4.0";false;'
--		@test $(GCCVERSIONMINOR) == 1 || sh -c 'echo "GCC version lower than 4.4.0";false;'
- 
- SOAPdenovo:	envTest $(OBJS)
- 		@printf "Linking...                                                \r"

Modified: trunk/packages/soap/soapdenovo2/trunk/debian/patches/series
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/series	2013-04-09 17:54:02 UTC (rev 13282)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/series	2013-04-10 15:17:22 UTC (rev 13283)
@@ -1,3 +1,2 @@
-fix_gcc_path
 fix_usage_name
 add_hardening

Modified: trunk/packages/soap/soapdenovo2/trunk/debian/watch
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/watch	2013-04-09 17:54:02 UTC (rev 13282)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/watch	2013-04-10 15:17:22 UTC (rev 13283)
@@ -1,5 +1,3 @@
 # Compulsory line, this is a version 3 file
 version=3
-http://qa.debian.org/watch/sf.php/soapdenovo2/SOAPdenovo2-src-r(.+)\.(?:zip|tgz|tbz2|txz|tar\.gz|tar\.bz2|tar\.xz)
-#http://sf.net/SOAPdenovo2/SOAPdenovo2-src-r(.+)\.(?:zip|tgz|tbz2|txz|tar\.gz|tar\.bz2|tar\.xz)
-#opts=filenamemangle=s/down\/SOAPdenovo-V/soapdenovo-/ http://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2/  down/SOAPdenovo-V(.*)\.src\.tgz
+opts="dversionmangle=s/\+dfsg//g" http://qa.debian.org/watch/sf.php/soapdenovo2/SOAPdenovo2-src-r(.+)\.(?:zip|tgz|tbz2|txz|tar\.gz|tar\.bz2|tar\.xz)

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