[med-svn] r14348 - in trunk/packages/soap/soapdenovo2/trunk/debian: . patches
Olivier Sallou
osallou at alioth.debian.org
Mon Aug 5 12:04:39 UTC 2013
Author: osallou
Date: 2013-08-05 12:04:39 +0000 (Mon, 05 Aug 2013)
New Revision: 14348
Added:
trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_compilation
Modified:
trunk/packages/soap/soapdenovo2/trunk/debian/changelog
trunk/packages/soap/soapdenovo2/trunk/debian/compat
trunk/packages/soap/soapdenovo2/trunk/debian/control
trunk/packages/soap/soapdenovo2/trunk/debian/install
trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening
trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name
trunk/packages/soap/soapdenovo2/trunk/debian/patches/series
trunk/packages/soap/soapdenovo2/trunk/debian/rules
Log:
new upstream release (2.4.0, update patches to new release, remove deprecated tags from control, update mion debhelper
Modified: trunk/packages/soap/soapdenovo2/trunk/debian/changelog
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/changelog 2013-08-05 11:46:09 UTC (rev 14347)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/changelog 2013-08-05 12:04:39 UTC (rev 14348)
@@ -1,3 +1,9 @@
+soapdenovo2 (240+dfsg-1) UNRELEASED; urgency=low
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> Thu, 27 Jun 2013 16:23:26 +0200
+
soapdenovo2 (223+dfsg-1) unstable; urgency=low
* debian/copyright:
Modified: trunk/packages/soap/soapdenovo2/trunk/debian/compat
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/compat 2013-08-05 11:46:09 UTC (rev 14347)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/compat 2013-08-05 12:04:39 UTC (rev 14348)
@@ -1 +1 @@
-8
+9
Modified: trunk/packages/soap/soapdenovo2/trunk/debian/control
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/control 2013-08-05 11:46:09 UTC (rev 14347)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/control 2013-08-05 12:04:39 UTC (rev 14348)
@@ -1,10 +1,9 @@
Source: soapdenovo2
Section: science
Priority: optional
-Build-Depends: debhelper (>= 8), hardening-includes, zlib1g-dev, libbam-dev, libaio-dev
+Build-Depends: debhelper (>= 9), 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
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/soap/soapdenovo2/trunk/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/soap/soapdenovo2/
Standards-Version: 3.9.3
Modified: trunk/packages/soap/soapdenovo2/trunk/debian/install
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/install 2013-08-05 11:46:09 UTC (rev 14347)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/install 2013-08-05 12:04:39 UTC (rev 14348)
@@ -1,2 +1,2 @@
-standardPregraph/SOAPdenovo-63mer usr/bin/
-standardPregraph/SOAPdenovo-127mer usr/bin/
+SOAPdenovo-63mer usr/bin/
+SOAPdenovo-127mer usr/bin/
Modified: trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening 2013-08-05 11:46:09 UTC (rev 14347)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening 2013-08-05 12:04:39 UTC (rev 14348)
@@ -6,25 +6,81 @@
Last-Updated: 2013-02-09
--- a/standardPregraph/Makefile
+++ b/standardPregraph/Makefile
-@@ -8,7 +8,11 @@
- 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`
+@@ -12,7 +12,11 @@
+ CFLAGS= -O0 -g -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
+ else
+ CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
++CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS`
+CFLAGS+=$(HARDENING_CFLAGS)
-+LDFLAGS = `dpkg-buildflags --get LDFLAGS`
+ endif
++LDFLAGS= `dpkg-buildflags --get LDFLAGS`
+LDFLAGS+=$(HARDENING_LDFLAGS)
DFLAGS=
OBJS= arc.o attachPEinfo.o bubble.o check.o compactEdge.o \
concatenateEdge.o connect.o contig.o cutTipPreGraph.o cutTip_graph.o \
-@@ -83,7 +87,7 @@
+@@ -87,9 +91,10 @@
+ @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)
+-SOAPdenovo: envTest $(OBJS)
++#SOAPdenovo: envTest $(OBJS)
++SOAPdenovo:
@printf "Linking... \r"
- @$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
+ @$(CC) $(CFLAGS) $(LDFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
@printf "$(PROG) compilation done.\n";
clean:
+--- a/sparsePregraph/Makefile
++++ b/sparsePregraph/Makefile
+@@ -3,7 +3,11 @@
+ CFLAGS= -O0 -g -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
+ else
+ CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
++CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS`
++CFLAGS+=$(HARDENING_CFLAGS)
+ endif
++LDFLAGS= `dpkg-buildflags --get LDFLAGS`
++LDFLAGS+=$(HARDENING_LDFLAGS)
+
+ DFLAGS=
+ OBJS= build_graph.o build_edge.o multi_threads.o \
+@@ -74,7 +78,7 @@
+
+ pregraph_sparse: clean envTest $(OBJS)
+ @printf "Linking... \r"
+- #@$(CC) $(CFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
++ #@$(CC) $(LDFLAGS) $(CFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
+ @printf "$(PROG) compilation done.\n";
+
+ clean:
+--- a/Makefile
++++ b/Makefile
+@@ -3,8 +3,13 @@
+ CFLAGS= -O0 -g -fomit-frame-pointer
+ else
+ CFLAGS= -O4 -fomit-frame-pointer
++CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS`
++CFLAGS+=$(HARDENING_CFLAGS)
+ endif
+
++LDFLAGS= `dpkg-buildflags --get LDFLAGS`
++LDFLAGS+=$(HARDENING_LDFLAGS)
++
+ SUBDIRS = sparsePregraph standardPregraph
+ PROG= SOAPdenovo-63mer SOAPdenovo-127mer
+ INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc
+@@ -64,11 +69,11 @@
+ SOAPdenovo-63mer:
+ @cd sparsePregraph;make 63mer=1;cd ..;
+ @cd standardPregraph;make 63mer=1;cd ..;
+- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
++ @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LDFLAGS) $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
+ SOAPdenovo-127mer:
+ @cd sparsePregraph;make 127mer=1;cd ..;
+ @cd standardPregraph;make 127mer=1;cd ..;
+- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
++ @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LDFLAGS) $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
+ clean:
+ @cd sparsePregraph;make clean;cd ..;
+ @cd standardPregraph;make clean;cd ..;
Added: trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_compilation
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_compilation (rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_compilation 2013-08-05 12:04:39 UTC (rev 14348)
@@ -0,0 +1,29 @@
+Subject: Fails to compile, usleep unknown
+Description: code from upstream fails to compile.
+ An include is missing.
+ Mail has been sent upstream and question posted to
+ their google group but got no answer.
+Forwarded: no
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2013-08-05
+--- a/sparsePregraph/pregraph_sparse.cpp
++++ b/sparsePregraph/pregraph_sparse.cpp
+@@ -32,6 +32,7 @@
+ #include "seq_util.h"
+ #include "convert_soapdenovo.h"
+
++#include <unistd.h>
+
+ static int LOAD_GRAPH = 0, BUILD_DBG = 1, BUILD_EDGES = 1, BUILD_PREARCS = 1;
+ //static int run_mode=0;
+--- a/sparsePregraph/inc/multi_threads.h
++++ b/sparsePregraph/inc/multi_threads.h
+@@ -24,6 +24,8 @@
+ #define _MULTI_THREADS_H
+ #include "stdinc.h"
+
++#include <unistd.h>
++
+ typedef struct parameter
+ {
+ unsigned char threadID;
Modified: trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name 2013-08-05 11:46:09 UTC (rev 14347)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name 2013-08-05 12:04:39 UTC (rev 14348)
@@ -7,12 +7,13 @@
Last-Updated: 2013-02-09
--- a/standardPregraph/main.c
+++ b/standardPregraph/main.c
-@@ -99,7 +99,7 @@
+@@ -104,7 +104,7 @@
static void display_usage ()
{
- fprintf ( stderr, "\nUsage: SOAPdenovo <command> [option]\n" );
+ fprintf ( stderr, "\nUsage: soapdenovo2-63mer/soapdenovo2-127mer <command> [option]\n" );
- fprintf ( stderr, " pregraph construct kmer-graph\n" );
- fprintf ( stderr, " contig eliminate errors and output contigs\n" );
- fprintf ( stderr, " map map reads to contigs\n" );
+ fprintf ( stderr, " pregraph construct kmer-graph\n" );
+ fprintf ( stderr, " sparse_pregraph construct sparse kmer-graph\n");
+ fprintf ( stderr, " contig eliminate errors and output contigs\n" );
+
Modified: trunk/packages/soap/soapdenovo2/trunk/debian/patches/series
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/series 2013-08-05 11:46:09 UTC (rev 14347)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/series 2013-08-05 12:04:39 UTC (rev 14348)
@@ -1,2 +1,3 @@
+fix_compilation
fix_usage_name
add_hardening
Modified: trunk/packages/soap/soapdenovo2/trunk/debian/rules
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/rules 2013-08-05 11:46:09 UTC (rev 14347)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/rules 2013-08-05 12:04:39 UTC (rev 14348)
@@ -18,11 +18,11 @@
%:
dh $@
-override_dh_auto_build:
- cd standardPregraph && make 63mer=1
- cd standardPregraph && make 127mer=1
+#override_dh_auto_build:
+# cd standardPregraph && make 63mer=1
+# cd standardPregraph && make 127mer=1
# cd sparsePregraph && make
- dh_auto_build
+# dh_auto_build
override_dh_install:
dh_install
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