[med-svn] r14354 - in trunk/packages/soap/soapdenovo2/tags: . 240+dfsg-1/debian 240+dfsg-1/debian/patches
Olivier Sallou
osallou at alioth.debian.org
Mon Aug 5 15:07:14 UTC 2013
Author: osallou
Date: 2013-08-05 15:07:14 +0000 (Mon, 05 Aug 2013)
New Revision: 14354
Added:
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/changelog
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/compat
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/control
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/copyright
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/install
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/add_hardening
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/fix_compilation
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/fix_usage_name
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/series
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/use_debian_zlib
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/use_libsam
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/rules
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/watch
Removed:
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/changelog
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/compat
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/control
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/copyright
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/install
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/add_hardening
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/fix_gcc_path
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/fix_usage_name
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/series
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/rules
trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/watch
Log:
[svn-buildpackage] Tagging soapdenovo2 240+dfsg-1
Deleted: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/changelog
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/changelog 2013-04-09 17:54:02 UTC (rev 13282)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/changelog 2013-08-05 15:07:14 UTC (rev 14354)
@@ -1,11 +0,0 @@
-soapdenovo2 (223-2) unstable; urgency=low
-
- * debian/copyright: Update copyright years and content
-
- -- Olivier Sallou <osallou at debian.org> Sat, 09 Feb 2013 13:02:55 +0100
-
-soapdenovo2 (223-1) unstable; 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/240+dfsg-1/debian/changelog (from rev 14353, trunk/packages/soap/soapdenovo2/trunk/debian/changelog)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/changelog (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/changelog 2013-08-05 15:07:14 UTC (rev 14354)
@@ -0,0 +1,29 @@
+soapdenovo2 (240+dfsg-1) unstable; 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:
+ remove .a files from upstream archive (Closes: #705139).
+ debian/patches:
+ update patches after lib removal
+ debian/control:
+ add bam and aio lib dependencies
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 10 Apr 2013 17:27:22 +0200
+
+soapdenovo2 (223-2) unstable; urgency=low
+
+ * debian/copyright:
+ Update copyright years and content,
+
+ -- Olivier Sallou <osallou at debian.org> Sat, 09 Feb 2013 13:02:55 +0100
+
+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/240+dfsg-1/debian/compat
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/compat 2013-04-09 17:54:02 UTC (rev 13282)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/compat 2013-08-05 15:07:14 UTC (rev 14354)
@@ -1 +0,0 @@
-8
Copied: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/compat (from rev 14348, trunk/packages/soap/soapdenovo2/trunk/debian/compat)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/compat (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/compat 2013-08-05 15:07:14 UTC (rev 14354)
@@ -0,0 +1 @@
+9
Deleted: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/control
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/control 2013-04-09 17:54:02 UTC (rev 13282)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/control 2013-08-05 15:07:14 UTC (rev 14354)
@@ -1,24 +0,0 @@
-Source: soapdenovo2
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 8), hardening-includes, zlib1g-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
-Homepage: http://soap.genomics.org.cn/soapdenovo.html
-
-Package: soapdenovo2
-Architecture: any-amd64 any-ppc64 any-ia64
-#Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, zlib1g
-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/240+dfsg-1/debian/control (from rev 14350, trunk/packages/soap/soapdenovo2/trunk/debian/control)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/control (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/control 2013-08-05 15:07:14 UTC (rev 14354)
@@ -0,0 +1,23 @@
+Source: soapdenovo2
+Section: science
+Priority: optional
+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>
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/soap/soapdenovo2/trunk/
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/soap/soapdenovo2/
+Standards-Version: 3.9.4
+Homepage: http://soap.genomics.org.cn/soapdenovo.html
+
+Package: soapdenovo2
+Architecture: any-amd64 any-ppc64 any-ia64
+#Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, zlib1g
+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.
Deleted: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/copyright
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/copyright 2013-04-09 17:54:02 UTC (rev 13282)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/copyright 2013-08-05 15:07:14 UTC (rev 14354)
@@ -1,84 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: soapdenovo
-Source: http://soap.genomics.org.cn/soapdenovo.html
-
-Files: standardPregraph/inc/bam.h standardPregraph/inc/faidx.h sparsePregraph/inc/bam.h sparsePregraph/inc/faidx.h
-Copyright: 2008 Genome Research Ltd (GRL)
-License: MIT
- Permission is hereby granted, free of charge, to any person obtaining a copy
- of this software and associated documentation files (the "Software"), to deal
- in the Software without restriction, including without limitation the rights
- to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- copies of the Software, and to permit persons to whom the Software is
- furnished to do so, subject to the following conditions:
- .
- The above copyright notice and this permission notice shall be included in
- all copies or substantial portions of the Software.
- .
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- THE SOFTWARE.
-
-Files: standardPregraph/inc/faidx.h sparsePregraph/inc/faidx.h
-Copyright: 2008 Broad Institute / Massachusetts Institute of Technology
-License: MIT
- Permission is hereby granted, free of charge, to any person obtaining a copy
- of this software and associated documentation files (the "Software"), to deal
- in the Software without restriction, including without limitation the rights
- to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- copies of the Software, and to permit persons to whom the Software is
- furnished to do so, subject to the following conditions:
- .
- The above copyright notice and this permission notice shall be included in
- all copies or substantial portions of the Software.
- .
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- THE SOFTWARE.
-
-
-Files: *
-Copyright: 2008-2012 BGI-Shenzhen
-License: GPL-3+
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
- .
- On Debian systems, the complete text of the GNU General
- Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
-
-Files: debian/*
-Copyright: 2012 Olivier Sallou <osallou at debian.org>
-License: GPL-2+
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
- .
- On Debian systems, the complete text of the GNU General
- Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
Copied: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/copyright (from rev 14352, trunk/packages/soap/soapdenovo2/trunk/debian/copyright)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/copyright (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/copyright 2013-08-05 15:07:14 UTC (rev 14354)
@@ -0,0 +1,98 @@
+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
+ standardPregraph/inc/sam.h
+ standardPregraph/inc/bam.h
+ standardPregraph/inc/bgzf.h
+ sparsePregraph/inc/sam.h
+ sparsePregraph/inc/bam.h
+ sparsePregraph/inc/bgzf.h
+ standardPregraph/inc/zlib.h
+ standardPregraph/inc/zconf.h
+ sparsePregraph/inc/zlib.h
+ sparsePregraph/inc/zconf.h
+ standardPregraph/inc/*.so
+ 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)
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
+Files: standardPregraph/inc/faidx.h sparsePregraph/inc/faidx.h
+Copyright: 2008 Broad Institute / Massachusetts Institute of Technology
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
+
+Files: *
+Copyright: 2008-2012 BGI-Shenzhen
+License: GPL-3+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+
+Files: debian/*
+Copyright: 2012 Olivier Sallou <osallou at debian.org>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
Deleted: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/install
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/install 2013-04-09 17:54:02 UTC (rev 13282)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/install 2013-08-05 15:07:14 UTC (rev 14354)
@@ -1,2 +0,0 @@
-standardPregraph/SOAPdenovo-63mer usr/bin/
-standardPregraph/SOAPdenovo-127mer usr/bin/
Copied: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/install (from rev 14348, trunk/packages/soap/soapdenovo2/trunk/debian/install)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/install (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/install 2013-08-05 15:07:14 UTC (rev 14354)
@@ -0,0 +1,2 @@
+SOAPdenovo-63mer usr/bin/
+SOAPdenovo-127mer usr/bin/
Deleted: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/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/tags/240+dfsg-1/debian/patches/add_hardening 2013-08-05 15:07:14 UTC (rev 14354)
@@ -1,30 +0,0 @@
-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:
Copied: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/add_hardening (from rev 14351, trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/add_hardening (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/add_hardening 2013-08-05 15:07:14 UTC (rev 14354)
@@ -0,0 +1,86 @@
+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
+@@ -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+=$(HARDENING_CFLAGS)
+ endif
++LDFLAGS= `dpkg-buildflags --get LDFLAGS`
++LDFLAGS+=$(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 \
+@@ -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 $(OBJS)
++SOAPdenovo:
+ @printf "Linking... \r"
+- @$(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 -I/usr/include/x86_64-linux-gnu
+@@ -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 ..;
Copied: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/fix_compilation (from rev 14351, trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_compilation)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/fix_compilation (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/fix_compilation 2013-08-05 15:07:14 UTC (rev 14354)
@@ -0,0 +1,40 @@
+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;
+--- a/Makefile
++++ b/Makefile
+@@ -7,7 +7,7 @@
+
+ SUBDIRS = sparsePregraph standardPregraph
+ PROG= SOAPdenovo-63mer SOAPdenovo-127mer
+-INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc
++INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc -I/usr/include/x86_64-linux-gnu
+
+ LIBPATH= -L/lib64 -L/usr/lib64 -L./sparsePregraph/inc -L./standardPregraph/inc
+ LIBS= -pthread -lz -lm
Deleted: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/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/tags/240+dfsg-1/debian/patches/fix_gcc_path 2013-08-05 15:07:14 UTC (rev 14354)
@@ -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"
Deleted: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/fix_usage_name
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name 2013-04-09 17:54:02 UTC (rev 13282)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/fix_usage_name 2013-08-05 15:07:14 UTC (rev 14354)
@@ -1,18 +0,0 @@
-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" );
Copied: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/fix_usage_name (from rev 14348, trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/fix_usage_name (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/fix_usage_name 2013-08-05 15:07:14 UTC (rev 14354)
@@ -0,0 +1,19 @@
+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
+@@ -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, " sparse_pregraph construct sparse kmer-graph\n");
+ fprintf ( stderr, " contig eliminate errors and output contigs\n" );
+
Deleted: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/series
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/series 2013-04-09 17:54:02 UTC (rev 13282)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/series 2013-08-05 15:07:14 UTC (rev 14354)
@@ -1,3 +0,0 @@
-fix_gcc_path
-fix_usage_name
-add_hardening
Copied: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/series (from rev 14352, trunk/packages/soap/soapdenovo2/trunk/debian/patches/series)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/series (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/series 2013-08-05 15:07:14 UTC (rev 14354)
@@ -0,0 +1,5 @@
+use_libsam
+fix_compilation
+fix_usage_name
+add_hardening
+use_debian_zlib
Copied: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/use_debian_zlib (from rev 14352, trunk/packages/soap/soapdenovo2/trunk/debian/patches/use_debian_zlib)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/use_debian_zlib (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/use_debian_zlib 2013-08-05 15:07:14 UTC (rev 14354)
@@ -0,0 +1,228 @@
+Subject: use Debian zlib library
+Description: Debian library is more recent than the one embedded upstream.
+ Its API changed and code needs to be updated to use this version.
+ See more info here:
+ http://www.postgresql.org/message-id/1329988571.6474.9.camel@vanquo.pezone.net
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2013-08-05
+Forwaded: no
+--- a/standardPregraph/prlRead2Ctg.c
++++ b/standardPregraph/prlRead2Ctg.c
+@@ -424,7 +424,7 @@
+ }
+ }
+
+-static void output1read_gz ( int t, gzFile * outfp, gzFile * outfp2, char orien, int dhflag )
++static void output1read_gz ( int t, gzFile outfp, gzFile outfp2, char orien, int dhflag )
+ {
+ int len = lenBuffer[t];
+ int index;
+@@ -500,7 +500,7 @@
+ fprintf ( outfp, "\n" );
+ }
+
+-static void getPEreadOnContig ( int t, gzFile * outfp )
++static void getPEreadOnContig ( int t, gzFile outfp )
+ {
+ int len1, len2, index;
+ char orien1, orien2;
+@@ -560,7 +560,7 @@
+ }
+ }*/
+
+-static void getReadIngap ( int t, int insSize, gzFile * outfp1, gzFile * outfp2, boolean readOne )
++static void getReadIngap ( int t, int insSize, gzFile outfp1, gzFile outfp2, boolean readOne )
+ {
+ int read1, read2;
+ char orientation;
+@@ -618,7 +618,7 @@
+ }
+ }
+
+-static void recordAlldgn ( gzFile * outfp, int * insSizeArr, gzFile * outfp1, gzFile * outfp2, gzFile * outfp4 )
++static void recordAlldgn ( gzFile outfp, int * insSizeArr, gzFile outfp1, gzFile outfp2, gzFile outfp4 )
+ {
+ int t, ctgId;
+ boolean rd1gap, rd2gap;
+@@ -773,7 +773,7 @@
+ long long i;
+ char * src_name, *next_name, name[256];
+ FILE * fo2;
+- gzFile * fo, *outfp1 = NULL, *outfp2 = NULL, *outfp3 = NULL, *outfp4 = NULL;
++ gzFile fo, outfp1 = NULL, outfp2 = NULL, outfp3 = NULL, outfp4 = NULL;
+ int maxReadNum, libNo, prevLibNo, insSize = 0;
+ boolean flag, pairs = 1;
+ pthread_t threads[thrd_num];
+--- a/standardPregraph/prlReadFillGap.c
++++ b/standardPregraph/prlReadFillGap.c
+@@ -104,7 +104,7 @@
+ free ( ( void * ) length_array );
+ }
+
+-static long long getRead1by1_gz ( gzFile * fp, DARRAY * readSeqInGap )
++static long long getRead1by1_gz ( gzFile fp, DARRAY * readSeqInGap )
+ {
+ long long readCounter = 0;
+
+@@ -206,7 +206,7 @@
+ static boolean loadReads4gap ( char * graphfile )
+ {
+ FILE * fp1, *fp2;
+- gzFile * fp;
++ gzFile fp;
+ char name[1024];
+ long long readCounter;
+
+--- a/standardPregraph/output_pregraph.c
++++ b/standardPregraph/output_pregraph.c
+@@ -85,7 +85,7 @@
+ fclose ( fp );
+ }
+
+-void output_1edge ( preEDGE * edge, gzFile * fp )
++void output_1edge ( preEDGE * edge, gzFile fp )
+ {
+ int i;
+ gzprintf ( fp, ">length %d,", edge->length );
+--- a/standardPregraph/orderContig.c
++++ b/standardPregraph/orderContig.c
+@@ -5072,7 +5072,7 @@
+ char name[256], *line;
+ FILE * fp1;
+ FILE * linkF;
+- gzFile * fp2;
++ gzFile fp2;
+ int i;
+ int flag = 0;
+ unsigned int j;
+--- a/standardPregraph/node2edge.c
++++ b/standardPregraph/node2edge.c
+@@ -37,8 +37,8 @@
+ static preEDGE temp_edge; // for temp use in merge_V2()
+ static char edge_seq[100000]; //use this static 'edge_seq ' as an temp seq in merge_V2() for speed ..
+
+-static void make_edge ( gzFile * fp );
+-static void merge_linearV2 ( char bal_edge, STACK * nStack, int count, gzFile * fp );
++static void make_edge ( gzFile fp );
++static void merge_linearV2 ( char bal_edge, STACK * nStack, int count, gzFile fp );
+ static int check_iden_kmerList ( STACK * stack1, STACK * stack2 );
+
+ //for stack
+@@ -60,7 +60,7 @@
+ *************************************************/
+ void kmer2edges ( char * outfile )
+ {
+- gzFile * fp;
++ gzFile fp;
+ char temp[256];
+ sprintf ( temp, "%s.edge.gz", outfile );
+ fp = gzopen ( temp, "w" );
+@@ -234,7 +234,7 @@
+ Return:
+ 0.
+ *************************************************/
+-static int startEdgeFromNode ( kmer_t * node1, gzFile * fp )
++static int startEdgeFromNode ( kmer_t * node1, gzFile fp )
+ {
+ int node_c, palindrome;
+ unsigned char flag;
+@@ -363,7 +363,7 @@
+ Return:
+ None.
+ *************************************************/
+-void make_edge ( gzFile * fp )
++void make_edge ( gzFile fp )
+ {
+ int i = 0;
+ kmer_t * node1;
+@@ -427,7 +427,7 @@
+ Return:
+ None.
+ *************************************************/
+-static void merge_linearV2 ( char bal_edge, STACK * nStack, int count, gzFile * fp )
++static void merge_linearV2 ( char bal_edge, STACK * nStack, int count, gzFile fp )
+ {
+ int length, char_index;
+ preEDGE * newedge;
+--- a/standardPregraph/loadPreGraph.c
++++ b/standardPregraph/loadPreGraph.c
+@@ -449,7 +449,7 @@
+ {
+ char c, name[256], line[1024], str[32];
+ char * tightSeq = NULL;
+- gzFile * fp;
++ gzFile fp;
+ Kmer from_kmer, to_kmer;
+ int n = 0, i, length, cvg, index = -1, bal_ed, edgeno;
+ int linelen;
+--- a/standardPregraph/kmer.c
++++ b/standardPregraph/kmer.c
+@@ -483,7 +483,7 @@
+ fprintf ( fp, "%c", c );
+ }
+
+-void print_kmer_gz ( gzFile * fp, Kmer kmer, char c )
++void print_kmer_gz ( gzFile fp, Kmer kmer, char c )
+ {
+ gzprintf ( fp, "%llx %llx %llx %llx", kmer.high1, kmer.low1, kmer.high2, kmer.low2 );
+ gzprintf ( fp, "%c", c );
+@@ -795,7 +795,7 @@
+ fprintf ( fp, "%c", c );
+ }
+
+-void print_kmer_gz ( gzFile * fp, Kmer kmer, char c )
++void print_kmer_gz ( gzFile fp, Kmer kmer, char c )
+ {
+ gzprintf ( fp, "%llx %llx", kmer.high, kmer.low );
+ gzprintf ( fp, "%c", c );
+--- a/standardPregraph/attachPEinfo.c
++++ b/standardPregraph/attachPEinfo.c
+@@ -492,7 +492,7 @@
+ Return:
+ Loaded alignment record number.
+ *************************************************/
+-int connectByPE_grad_gz ( gzFile * fp, int peGrad, char * line )
++int connectByPE_grad_gz ( gzFile fp, int peGrad, char * line )
+ {
+ long long pre_readno, readno, minno, maxno;
+ int pre_pos, pos, flag, PE, count = 0, Total_PE = 0;
+--- a/standardPregraph/inc/extfunc.h
++++ b/standardPregraph/inc/extfunc.h
+@@ -79,10 +79,10 @@
+ extern int putInsertS ( long long readid, int size, int * currGrads );
+ extern int getInsertS ( long long readid, int * readlen );
+ extern int connectByPE_grad ( FILE * fp, int peGrad, char * line );
+-extern int connectByPE_grad_gz ( gzFile * fp, int peGrad, char * line );
++extern int connectByPE_grad_gz ( gzFile fp, int peGrad, char * line );
+ extern void PEgradsScaf ( char * infile );
+ extern void reorderAnnotation ( char * infile, char * outfile );
+-extern void output_1edge ( preEDGE * edge, gzFile * fp );
++extern void output_1edge ( preEDGE * edge, gzFile fp );
+ extern void prlRead2edge ( char * libfile, char * outfile );
+ extern void annotFileTrans ( char * infile, char * outfile );
+ extern void prlLoadPath ( char * graphfile );
+--- a/standardPregraph/hashFunction.c
++++ b/standardPregraph/hashFunction.c
+@@ -82,7 +82,7 @@
+ };
+
+ typedef int ( *CRC32CFunctionPtr ) ( uint32_t, const char *, size_t );
+-static CRC32CFunctionPtr crc32;
++static CRC32CFunctionPtr s_crc32;
+
+ static uint32_t cpuid ( uint32_t functionInput )
+ {
+@@ -145,11 +145,11 @@
+
+ ubyte8 hash_kmer ( Kmer kmer )
+ {
+- return ( crc32 ( 0, ( char * ) &kmer, sizeof ( Kmer ) ) );
++ return ( s_crc32 ( 0, ( char * ) &kmer, sizeof ( Kmer ) ) );
+ }
+
+ void crc32c_Init()
+ {
+- crc32 = detectBestCRC32C();
++ s_crc32 = detectBestCRC32C();
+ }
+
Copied: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/use_libsam (from rev 14352, trunk/packages/soap/soapdenovo2/trunk/debian/patches/use_libsam)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/use_libsam (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/patches/use_libsam 2013-08-05 15:07:14 UTC (rev 14354)
@@ -0,0 +1,42 @@
+Subject: upstream copies libsam headers
+Description: use Debian libraries instead of embedded headers
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2013-08-05
+Forwarded: no
+--- a/sparsePregraph/Makefile
++++ b/sparsePregraph/Makefile
+@@ -10,7 +10,7 @@
+ build_preArc.o pregraph_sparse.o io_func.o\
+ global.o convert_soapdenovo.o
+ PROG=
+-INCLUDES= -I./inc
++INCLUDES= -I./inc -I/usr/include/samtools
+ SUBDIRS= .
+ LIBPATH= -L/usr/lib64
+ LIBS= -pthread -lz -L./inc
+--- a/sparsePregraph/inc/stdinc.h
++++ b/sparsePregraph/inc/stdinc.h
+@@ -39,4 +39,4 @@
+
+
+
+-
++#include <stdbool.h>
+--- a/standardPregraph/Makefile
++++ b/standardPregraph/Makefile
+@@ -25,7 +25,7 @@
+ readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o \
+ cutTip_graph2.o linearEdge.o kmerhash.o read2edge.o iterate.o
+ PROG= SOAPdenovo-63mer
+-INCLUDES= -Iinc
++INCLUDES= -Iinc -I/usr/include/samtools
+ SUBDIRS= .
+ LIBPATH= -L/lib64 -L/usr/lib64 -L./inc
+ LIBS= -pthread -lz -lm
+--- a/standardPregraph/inc/stdinc.h
++++ b/standardPregraph/inc/stdinc.h
+@@ -32,3 +32,4 @@
+ #include "types.h"
+ #include <aio.h>
+ #include <errno.h>
++#include <stdbool.h>
Deleted: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/rules
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/rules 2013-04-09 17:54:02 UTC (rev 13282)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/rules 2013-08-05 15:07:14 UTC (rev 14354)
@@ -1,34 +0,0 @@
-#!/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 $@
-
-override_dh_auto_build:
- cd standardPregraph && make 63mer=1
- cd standardPregraph && make 127mer=1
-# cd sparsePregraph && make
- dh_auto_build
-
-override_dh_install:
- dh_install
- cd debian/soapdenovo2/usr/bin/;rename 's/SOAPdenovo/soapdenovo2/' SOAP*
-
-override_dh_clean:
- cd standardPregraph && make 63mer=1 clean && make 127mer=1 clean
- cd sparsePregraph && make clean
- dh_clean
Copied: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/rules (from rev 14348, trunk/packages/soap/soapdenovo2/trunk/debian/rules)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/rules (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/rules 2013-08-05 15:07:14 UTC (rev 14354)
@@ -0,0 +1,34 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+export DEB_BUILD_HARDENING=1
+export DEB_BUILD_HARDENING_FORTIFY=1
+
+include /usr/share/hardening-includes/hardening.make
+
+CFLAGS=$(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
Deleted: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/watch
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/watch 2013-04-09 17:54:02 UTC (rev 13282)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/watch 2013-08-05 15:07:14 UTC (rev 14354)
@@ -1,5 +0,0 @@
-# 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
Copied: trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/watch (from rev 13283, trunk/packages/soap/soapdenovo2/trunk/debian/watch)
===================================================================
--- trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/watch (rev 0)
+++ trunk/packages/soap/soapdenovo2/tags/240+dfsg-1/debian/watch 2013-08-05 15:07:14 UTC (rev 14354)
@@ -0,0 +1,3 @@
+# Compulsory line, this is a version 3 file
+version=3
+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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