[med-svn] [soapdenovo2] 04/09: Imported Debian patch 223+dfsg-1
Sascha Steinbiss
sascha at steinbiss.name
Fri May 27 22:37:08 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository soapdenovo2.
commit ebdcf676c430326fb3e0f3451844a44138ea0568
Merge: d05f5be 4422d01
Author: Olivier Sallou <osallou at debian.org>
Date: Wed Apr 10 17:27:22 2013 +0200
Imported Debian patch 223+dfsg-1
LICENSE | 0
MANUAL | 0
debian/changelog | 14 ++++++++++-
debian/control | 2 +-
debian/copyright | 3 +++
debian/patches/add_hardening | 8 +++----
debian/patches/fix_gcc_path | 41 --------------------------------
debian/patches/series | 1 -
debian/watch | 4 +---
sparsePregraph/Makefile | 4 ++--
sparsePregraph/build_edge.cpp | 0
sparsePregraph/build_graph.cpp | 0
sparsePregraph/build_preArc.cpp | 0
sparsePregraph/convert_soapdenovo.cpp | 0
sparsePregraph/global.cpp | 0
sparsePregraph/inc/bam.h | 0
sparsePregraph/inc/bgzf.h | 0
sparsePregraph/inc/build_edge.h | 0
sparsePregraph/inc/build_graph.h | 0
sparsePregraph/inc/build_preArc.h | 0
sparsePregraph/inc/convert_soapdenovo.h | 0
sparsePregraph/inc/core.h | 0
sparsePregraph/inc/faidx.h | 0
sparsePregraph/inc/glf.h | 0
sparsePregraph/inc/global.h | 0
sparsePregraph/inc/io_func.h | 0
sparsePregraph/inc/knetfile.h | 0
sparsePregraph/inc/kstring.h | 0
sparsePregraph/inc/libbam.a | Bin 872084 -> 0 bytes
sparsePregraph/inc/libbammac.a | Bin 636664 -> 0 bytes
sparsePregraph/inc/multi_threads.h | 0
sparsePregraph/inc/razf.h | 0
sparsePregraph/inc/sam.h | 0
sparsePregraph/inc/sam_header.h | 0
sparsePregraph/inc/sam_view.h | 0
sparsePregraph/inc/seq_util.h | 0
sparsePregraph/inc/sparse_kmer.h | 0
sparsePregraph/inc/spinLock.h | 0
sparsePregraph/inc/stdinc.h | 0
sparsePregraph/inc/xcurses.h | 0
sparsePregraph/inc/zconf.h | 0
sparsePregraph/inc/zlib.h | 0
sparsePregraph/io_func.cpp | 0
sparsePregraph/make.sh | 0
sparsePregraph/multi_threads.cpp | 0
sparsePregraph/pregraph_sparse.cpp | 0
standardPregraph/INSTALL | 0
standardPregraph/Makefile | 12 +++++-----
standardPregraph/VERSION | 0
standardPregraph/arc.c | 0
standardPregraph/attachPEinfo.c | 0
standardPregraph/bubble.c | 0
standardPregraph/change.log | 0
standardPregraph/check.c | 0
standardPregraph/compactEdge.c | 0
standardPregraph/concatenateEdge.c | 0
standardPregraph/connect.c | 0
standardPregraph/contig.c | 0
standardPregraph/cutTipPreGraph.c | 0
standardPregraph/cutTip_graph.c | 0
standardPregraph/cutTip_graph2.c | 0
standardPregraph/darray.c | 0
standardPregraph/dfib.c | 0
standardPregraph/dfibHeap.c | 0
standardPregraph/fib.c | 0
standardPregraph/fibHeap.c | 0
standardPregraph/hashFunction.c | 0
standardPregraph/inc/bam.h | 0
standardPregraph/inc/bgzf.h | 0
standardPregraph/inc/check.h | 0
standardPregraph/inc/darray.h | 0
standardPregraph/inc/def.h | 0
standardPregraph/inc/def2.h | 0
standardPregraph/inc/dfib.h | 0
standardPregraph/inc/dfibHeap.h | 0
standardPregraph/inc/dfibpriv.h | 0
standardPregraph/inc/extfunc.h | 0
standardPregraph/inc/extfunc2.h | 0
standardPregraph/inc/extvab.h | 0
standardPregraph/inc/faidx.h | 0
standardPregraph/inc/fib.h | 0
standardPregraph/inc/fibHeap.h | 0
standardPregraph/inc/fibpriv.h | 0
standardPregraph/inc/glf.h | 0
standardPregraph/inc/global.h | 0
standardPregraph/inc/kmerhash.h | 0
standardPregraph/inc/knetfile.h | 0
standardPregraph/inc/kstring.h | 0
standardPregraph/inc/libbam.a | Bin 872084 -> 0 bytes
standardPregraph/inc/libbammac.a | Bin 636664 -> 0 bytes
standardPregraph/inc/newhash.h | 0
standardPregraph/inc/nuc.h | 0
standardPregraph/inc/razf.h | 0
standardPregraph/inc/sam.h | 0
standardPregraph/inc/sam_header.h | 0
standardPregraph/inc/sam_view.h | 0
standardPregraph/inc/stack.h | 0
standardPregraph/inc/stdinc.h | 0
standardPregraph/inc/types.h | 0
standardPregraph/inc/xcurses.h | 0
standardPregraph/inc/zconf.h | 0
standardPregraph/inc/zlib.h | 0
standardPregraph/iterate.c | 0
standardPregraph/kmer.c | 0
standardPregraph/kmerhash.c | 0
standardPregraph/lib.c | 0
standardPregraph/linearEdge.c | 0
standardPregraph/loadGraph.c | 0
standardPregraph/loadPath.c | 0
standardPregraph/loadPreGraph.c | 0
standardPregraph/localAsm.c | 0
standardPregraph/main.c | 0
standardPregraph/make.sh | 0
standardPregraph/makeclean.sh | 0
standardPregraph/map.c | 0
standardPregraph/mem_manager.c | 0
standardPregraph/newhash.c | 0
standardPregraph/node2edge.c | 0
standardPregraph/orderContig.c | 0
standardPregraph/output_contig.c | 0
standardPregraph/output_pregraph.c | 0
standardPregraph/output_scaffold.c | 0
standardPregraph/pregraph.c | 0
standardPregraph/prlHashCtg.c | 0
standardPregraph/prlHashReads.c | 0
standardPregraph/prlRead2Ctg.c | 0
standardPregraph/prlRead2path.c | 0
standardPregraph/prlReadFillGap.c | 0
standardPregraph/read2edge.c | 0
standardPregraph/read2scaf.c | 0
standardPregraph/readInterval.c | 0
standardPregraph/readseq1by1.c | 0
standardPregraph/scaffold.c | 0
standardPregraph/searchPath.c | 0
standardPregraph/seperateScaff.pl | 0
standardPregraph/seq.c | 0
standardPregraph/splitReps.c | 0
standardPregraph/stack.c | 0
update.log | 0
139 files changed, 30 insertions(+), 59 deletions(-)
diff --cc debian/changelog
index 402464d,0000000..9ead6b8
mode 100644,000000..100644
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,11 -1,0 +1,23 @@@
++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
++ * 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
diff --cc debian/control
index fa5d487,0000000..03e0d6c
mode 100644,000000..100644
--- a/debian/control
+++ b/debian/control
@@@ -1,24 -1,0 +1,24 @@@
+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
+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.
diff --cc debian/copyright
index 7b2a0a0,0000000..9d90db9
mode 100644,000000..100644
--- a/debian/copyright
+++ b/debian/copyright
@@@ -1,84 -1,0 +1,87 @@@
+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)
+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".
diff --cc debian/patches/add_hardening
index 58f61a2,0000000..8b27d1d
mode 100644,000000..100644
--- a/debian/patches/add_hardening
+++ b/debian/patches/add_hardening
@@@ -1,30 -1,0 +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)
++ 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`
++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 @@
++@@ -83,7 +87,7 @@
+
+ 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:
diff --cc debian/patches/series
index f16b422,0000000..8666706
mode 100644,000000..100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@@ -1,3 -1,0 +1,2 @@@
- fix_gcc_path
+fix_usage_name
+add_hardening
diff --cc debian/watch
index 9854904,0000000..613d606
mode 100644,000000..100644
--- a/debian/watch
+++ b/debian/watch
@@@ -1,5 -1,0 +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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