[med-svn] r12970 - in trunk/packages/soap/soapdenovo2/tags: . 223-1/debian 223-1/debian/patches
Olivier Sallou
osallou at alioth.debian.org
Sat Feb 9 12:02:54 UTC 2013
Author: osallou
Date: 2013-02-09 12:02:54 +0000 (Sat, 09 Feb 2013)
New Revision: 12970
Added:
trunk/packages/soap/soapdenovo2/tags/223-1/
trunk/packages/soap/soapdenovo2/tags/223-1/debian/README.Debian
trunk/packages/soap/soapdenovo2/tags/223-1/debian/changelog
trunk/packages/soap/soapdenovo2/tags/223-1/debian/control
trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/add_hardening
trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_gcc_path
trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_usage_name
trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/series
trunk/packages/soap/soapdenovo2/tags/223-1/debian/rules
Removed:
trunk/packages/soap/soapdenovo2/tags/223-1/debian/README.Debian
trunk/packages/soap/soapdenovo2/tags/223-1/debian/changelog
trunk/packages/soap/soapdenovo2/tags/223-1/debian/control
trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_gcc_path
trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_usage_name
trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/series
trunk/packages/soap/soapdenovo2/tags/223-1/debian/rules
Log:
[svn-buildpackage] Tagging soapdenovo2 223-1
Deleted: trunk/packages/soap/soapdenovo2/tags/223-1/debian/README.Debian
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/README.Debian 2013-02-09 10:56:54 UTC (rev 12964)
+++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/README.Debian 2013-02-09 12:02:54 UTC (rev 12970)
@@ -1,9 +0,0 @@
-* SOAPdenovo2
-
-Binaries are soapdenovo2-63mer and soapdenovo2-127mer.
-See manpage for further explanations
-
-SparsePregraph does not compile from source, as such binaries are not provided.
-
- -- Olivier Sallou <osallou at debian.org> Sat, 09 Feb 2013 10:40:45 +0100
-
Copied: trunk/packages/soap/soapdenovo2/tags/223-1/debian/README.Debian (from rev 12965, trunk/packages/soap/soapdenovo2/trunk/debian/README.Debian)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/223-1/debian/README.Debian (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/README.Debian 2013-02-09 12:02:54 UTC (rev 12970)
@@ -0,0 +1,9 @@
+* SOAPdenovo2
+
+Binaries are soapdenovo2-63mer and soapdenovo2-127mer.
+See manpage soapdenovo2 for further explanations
+
+SparsePregraph does not compile from source, as such binaries are not provided.
+
+ -- Olivier Sallou <osallou at debian.org> Sat, 09 Feb 2013 10:40:45 +0100
+
Deleted: trunk/packages/soap/soapdenovo2/tags/223-1/debian/changelog
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/changelog 2013-02-09 10:56:54 UTC (rev 12964)
+++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/changelog 2013-02-09 12:02:54 UTC (rev 12970)
@@ -1,5 +0,0 @@
-soapdenovo2 (223-1) UNRELEASED; urgency=low
-
- * Initial release (Closes: #700160)
-
- -- Olivier Sallou <osallou at debian.org> Sat, 09 Feb 2013 10:40:45 +0100
Copied: trunk/packages/soap/soapdenovo2/tags/223-1/debian/changelog (from rev 12967, trunk/packages/soap/soapdenovo2/trunk/debian/changelog)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/223-1/debian/changelog (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/changelog 2013-02-09 12:02:54 UTC (rev 12970)
@@ -0,0 +1,5 @@
+soapdenovo2 (223-1) unstable; urgency=low
+
+ * Initial release (Closes: #700160)
+
+ -- Olivier Sallou <osallou at debian.org> Sat, 09 Feb 2013 10:40:45 +0100
Deleted: trunk/packages/soap/soapdenovo2/tags/223-1/debian/control
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/control 2013-02-09 10:56:54 UTC (rev 12964)
+++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/control 2013-02-09 12:02:54 UTC (rev 12970)
@@ -1,24 +0,0 @@
-Source: soapdenovo2
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 8),g++
-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
-Homepage: http://soap.genomics.org.cn/soapdenovo.html
-
-Package: soapdenovo2
-Architecture: any-amd64 any-ppc64 any-ia64
-#Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: short-read assembly method to build de novo draft assembly
- SOAPdenovo is a novel short-read assembly method that can build a de novo draft
- assembly for the human-sized genomes. The program is specially designed to
- assemble Illumina GA short reads.
- .
- It creates new opportunities for building reference
- sequences and carrying out accurate analyses of unexplored genomes in a cost
- effective way.
Copied: trunk/packages/soap/soapdenovo2/tags/223-1/debian/control (from rev 12968, trunk/packages/soap/soapdenovo2/trunk/debian/control)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/223-1/debian/control (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/control 2013-02-09 12:02:54 UTC (rev 12970)
@@ -0,0 +1,24 @@
+Source: soapdenovo2
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 8), hardening-includes
+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
+Homepage: http://soap.genomics.org.cn/soapdenovo.html
+
+Package: soapdenovo2
+Architecture: any-amd64 any-ppc64 any-ia64
+#Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: short-read assembly method to build de novo draft assembly
+ SOAPdenovo is a novel short-read assembly method that can build a de novo draft
+ assembly for the human-sized genomes. The program is specially designed to
+ assemble Illumina GA short reads.
+ .
+ It creates new opportunities for building reference
+ sequences and carrying out accurate analyses of unexplored genomes in a cost
+ effective way.
Copied: trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/add_hardening (from rev 12969, trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/add_hardening (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/add_hardening 2013-02-09 12:02:54 UTC (rev 12970)
@@ -0,0 +1,30 @@
+Subject: add fortify flags
+Description: Makefile does not load CFLAGS
+ from env, add extra flags for debian fortify
+Forwarded: no
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2013-02-09
+--- 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)
+-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`
++CFLAGS+=$(HARDENING_CFLAGS)
++LDFLAGS = `dpkg-buildflags --get LDFLAGS`
++LDFLAGS+=$(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 \
+@@ -81,7 +85,7 @@
+
+ SOAPdenovo: envTest $(OBJS)
+ @printf "Linking... \r"
+- @$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
++ @$(CC) $(CFLAGS) $(LDFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
+ @printf "$(PROG) compilation done.\n";
+
+ clean:
Deleted: trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_gcc_path
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_gcc_path 2013-02-09 10:56:54 UTC (rev 12964)
+++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_gcc_path 2013-02-09 12:02:54 UTC (rev 12970)
@@ -1,36 +0,0 @@
---- 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"
Copied: trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_gcc_path (from rev 12965, trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_gcc_path)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_gcc_path (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_gcc_path 2013-02-09 12:02:54 UTC (rev 12970)
@@ -0,0 +1,41 @@
+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"
Deleted: trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_usage_name
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name 2013-02-09 10:56:54 UTC (rev 12964)
+++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_usage_name 2013-02-09 12:02:54 UTC (rev 12970)
@@ -1,11 +0,0 @@
---- a/standardPregraph/main.c
-+++ b/standardPregraph/main.c
-@@ -99,7 +99,7 @@
-
- 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" );
Copied: trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_usage_name (from rev 12965, trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_usage_name (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/fix_usage_name 2013-02-09 12:02:54 UTC (rev 12970)
@@ -0,0 +1,18 @@
+Subject: update binary name
+Description: usage show SOAPdenovo binary name
+ while generated binaries are kmer dependent.
+ Debian modification to lowercase applied too.
+Forwarded: no
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2013-02-09
+--- a/standardPregraph/main.c
++++ b/standardPregraph/main.c
+@@ -99,7 +99,7 @@
+
+ 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" );
Deleted: trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/series
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/series 2013-02-09 10:56:54 UTC (rev 12964)
+++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/series 2013-02-09 12:02:54 UTC (rev 12970)
@@ -1,2 +0,0 @@
-fix_gcc_path
-fix_usage_name
Copied: trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/series (from rev 12967, trunk/packages/soap/soapdenovo2/trunk/debian/patches/series)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/series (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/patches/series 2013-02-09 12:02:54 UTC (rev 12970)
@@ -0,0 +1,3 @@
+fix_gcc_path
+fix_usage_name
+add_hardening
Deleted: trunk/packages/soap/soapdenovo2/tags/223-1/debian/rules
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/rules 2013-02-09 10:56:54 UTC (rev 12964)
+++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/rules 2013-02-09 12:02:54 UTC (rev 12970)
@@ -1,23 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-%:
- dh $@
-
-override_dh_auto_build:
- cd standardPregraph && make 63mer=1
- cd standardPregraph && make 127mer=1
-# cd sparsePregraph && make
- dh_auto_build
-
-override_dh_install:
- dh_install
- cd debian/soapdenovo2/usr/bin/;rename 's/SOAPdenovo/soapdenovo2/' SOAP*
-
-override_dh_clean:
- cd standardPregraph && make 63mer=1 clean && make 127mer=1 clean
- cd sparsePregraph && make clean
- dh_clean
Copied: trunk/packages/soap/soapdenovo2/tags/223-1/debian/rules (from rev 12967, trunk/packages/soap/soapdenovo2/trunk/debian/rules)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/223-1/debian/rules (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/223-1/debian/rules 2013-02-09 12:02:54 UTC (rev 12970)
@@ -0,0 +1,34 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+export DEB_BUILD_HARDENING=1
+export DEB_BUILD_HARDENING_FORTIFY=1
+
+include /usr/share/hardening-includes/hardening.make
+
+CFLAGS=$(shell dpkg-buildflags --get CFLAGS)
+LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)
+CFLAGS+=$(HARDENING_CFLAGS)
+CXXFLAGS+=$(HARDENING_CXXFLAGS)
+LDFLAGS+=$(HARDENING_LDFLAGS)
+
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ cd standardPregraph && make 63mer=1
+ cd standardPregraph && make 127mer=1
+# cd sparsePregraph && make
+ dh_auto_build
+
+override_dh_install:
+ dh_install
+ cd debian/soapdenovo2/usr/bin/;rename 's/SOAPdenovo/soapdenovo2/' SOAP*
+
+override_dh_clean:
+ cd standardPregraph && make 63mer=1 clean && make 127mer=1 clean
+ cd sparsePregraph && make clean
+ dh_clean
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