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 <[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 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 <[email protected]> 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 <[email protected]> Wed, 10 Apr 2013 17:27:22 +0200 + +soapdenovo2 (223-2) unstable; urgency=low + + * 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 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 <[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. 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 <[email protected]> +Uploaders: Olivier Sallou <[email protected]> +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 <[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". 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 <[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". 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 <[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) --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 <[email protected]> +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 <[email protected]> +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 <[email protected]> -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 <[email protected]> -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 <[email protected]> +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/[email protected] +Author: Olivier Sallou <[email protected]> +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 <[email protected]> +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) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
