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commit ebdcf676c430326fb3e0f3451844a44138ea0568 Merge: d05f5be 4422d01 Author: Olivier Sallou <[email protected]> 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 <[email protected]> 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 <[email protected]> Sat, 09 Feb 2013 13:02:55 +0100 + +soapdenovo2 (223-1) unstable; urgency=low + + * Initial release (Closes: #700160) + + -- Olivier Sallou <[email protected]> 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 <[email protected]> +Uploaders: Olivier Sallou <[email protected]> +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 <[email protected]> +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 <[email protected]> +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) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/soapdenovo2.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
