Author: osallou Date: 2013-08-05 12:04:39 +0000 (Mon, 05 Aug 2013) New Revision: 14348
Added: trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_compilation Modified: trunk/packages/soap/soapdenovo2/trunk/debian/changelog trunk/packages/soap/soapdenovo2/trunk/debian/compat trunk/packages/soap/soapdenovo2/trunk/debian/control trunk/packages/soap/soapdenovo2/trunk/debian/install trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name trunk/packages/soap/soapdenovo2/trunk/debian/patches/series trunk/packages/soap/soapdenovo2/trunk/debian/rules Log: new upstream release (2.4.0, update patches to new release, remove deprecated tags from control, update mion debhelper Modified: trunk/packages/soap/soapdenovo2/trunk/debian/changelog =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/changelog 2013-08-05 11:46:09 UTC (rev 14347) +++ trunk/packages/soap/soapdenovo2/trunk/debian/changelog 2013-08-05 12:04:39 UTC (rev 14348) @@ -1,3 +1,9 @@ +soapdenovo2 (240+dfsg-1) UNRELEASED; urgency=low + + * New upstream release + + -- Olivier Sallou <osal...@debian.org> Thu, 27 Jun 2013 16:23:26 +0200 + soapdenovo2 (223+dfsg-1) unstable; urgency=low * debian/copyright: Modified: trunk/packages/soap/soapdenovo2/trunk/debian/compat =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/compat 2013-08-05 11:46:09 UTC (rev 14347) +++ trunk/packages/soap/soapdenovo2/trunk/debian/compat 2013-08-05 12:04:39 UTC (rev 14348) @@ -1 +1 @@ -8 +9 Modified: trunk/packages/soap/soapdenovo2/trunk/debian/control =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/control 2013-08-05 11:46:09 UTC (rev 14347) +++ trunk/packages/soap/soapdenovo2/trunk/debian/control 2013-08-05 12:04:39 UTC (rev 14348) @@ -1,10 +1,9 @@ Source: soapdenovo2 Section: science Priority: optional -Build-Depends: debhelper (>= 8), hardening-includes, zlib1g-dev, libbam-dev, libaio-dev +Build-Depends: debhelper (>= 9), hardening-includes, zlib1g-dev, libbam-dev, libaio-dev Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Uploaders: Olivier Sallou <osal...@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 Modified: trunk/packages/soap/soapdenovo2/trunk/debian/install =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/install 2013-08-05 11:46:09 UTC (rev 14347) +++ trunk/packages/soap/soapdenovo2/trunk/debian/install 2013-08-05 12:04:39 UTC (rev 14348) @@ -1,2 +1,2 @@ -standardPregraph/SOAPdenovo-63mer usr/bin/ -standardPregraph/SOAPdenovo-127mer usr/bin/ +SOAPdenovo-63mer usr/bin/ +SOAPdenovo-127mer usr/bin/ Modified: trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening 2013-08-05 11:46:09 UTC (rev 14347) +++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening 2013-08-05 12:04:39 UTC (rev 14348) @@ -6,25 +6,81 @@ Last-Updated: 2013-02-09 --- a/standardPregraph/Makefile +++ b/standardPregraph/Makefile -@@ -8,7 +8,11 @@ - 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` +@@ -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+=$(HARDENING_CFLAGS) -+LDFLAGS = `dpkg-buildflags --get LDFLAGS` + endif ++LDFLAGS= `dpkg-buildflags --get LDFLAGS` +LDFLAGS+=$(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 \ -@@ -83,7 +87,7 @@ +@@ -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: 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 +@@ -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 ..; Added: trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_compilation =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_compilation (rev 0) +++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_compilation 2013-08-05 12:04:39 UTC (rev 14348) @@ -0,0 +1,29 @@ +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 <osal...@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; Modified: trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name 2013-08-05 11:46:09 UTC (rev 14347) +++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_usage_name 2013-08-05 12:04:39 UTC (rev 14348) @@ -7,12 +7,13 @@ Last-Updated: 2013-02-09 --- a/standardPregraph/main.c +++ b/standardPregraph/main.c -@@ -99,7 +99,7 @@ +@@ -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, " contig eliminate errors and output contigs\n" ); - fprintf ( stderr, " map map reads to contigs\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" ); + Modified: trunk/packages/soap/soapdenovo2/trunk/debian/patches/series =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/patches/series 2013-08-05 11:46:09 UTC (rev 14347) +++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/series 2013-08-05 12:04:39 UTC (rev 14348) @@ -1,2 +1,3 @@ +fix_compilation fix_usage_name add_hardening Modified: trunk/packages/soap/soapdenovo2/trunk/debian/rules =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/rules 2013-08-05 11:46:09 UTC (rev 14347) +++ trunk/packages/soap/soapdenovo2/trunk/debian/rules 2013-08-05 12:04:39 UTC (rev 14348) @@ -18,11 +18,11 @@ %: dh $@ -override_dh_auto_build: - cd standardPregraph && make 63mer=1 - cd standardPregraph && make 127mer=1 +#override_dh_auto_build: +# cd standardPregraph && make 63mer=1 +# cd standardPregraph && make 127mer=1 # cd sparsePregraph && make - dh_auto_build +# dh_auto_build override_dh_install: dh_install _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
