Author: osallou Date: 2013-04-10 15:17:22 +0000 (Wed, 10 Apr 2013) New Revision: 13283
Removed: trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_gcc_path Modified: trunk/packages/soap/soapdenovo2/trunk/debian/changelog trunk/packages/soap/soapdenovo2/trunk/debian/control trunk/packages/soap/soapdenovo2/trunk/debian/copyright trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening trunk/packages/soap/soapdenovo2/trunk/debian/patches/series trunk/packages/soap/soapdenovo2/trunk/debian/watch Log: remove .a files from upstream archive and updates patches Modified: trunk/packages/soap/soapdenovo2/trunk/debian/changelog =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/changelog 2013-04-09 17:54:02 UTC (rev 13282) +++ trunk/packages/soap/soapdenovo2/trunk/debian/changelog 2013-04-10 15:17:22 UTC (rev 13283) @@ -1,4 +1,4 @@ -soapdenovo2 (223-2) unstable; urgency=low +soapdenovo2 (223+dfsg-2) unstable; urgency=low * debian/copyright: Update copyright years and content Modified: trunk/packages/soap/soapdenovo2/trunk/debian/control =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/control 2013-04-09 17:54:02 UTC (rev 13282) +++ trunk/packages/soap/soapdenovo2/trunk/debian/control 2013-04-10 15:17:22 UTC (rev 13283) @@ -1,7 +1,7 @@ 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 Modified: trunk/packages/soap/soapdenovo2/trunk/debian/copyright =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/copyright 2013-04-09 17:54:02 UTC (rev 13282) +++ trunk/packages/soap/soapdenovo2/trunk/debian/copyright 2013-04-10 15:17:22 UTC (rev 13283) @@ -1,6 +1,9 @@ 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) Modified: trunk/packages/soap/soapdenovo2/trunk/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/trunk/debian/patches/add_hardening 2013-04-10 15:17:22 UTC (rev 13283) @@ -7,9 +7,9 @@ --- 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` @@ -19,7 +19,7 @@ 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" Deleted: trunk/packages/soap/soapdenovo2/trunk/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/trunk/debian/patches/fix_gcc_path 2013-04-10 15:17:22 UTC (rev 13283) @@ -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" Modified: trunk/packages/soap/soapdenovo2/trunk/debian/patches/series =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/patches/series 2013-04-09 17:54:02 UTC (rev 13282) +++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/series 2013-04-10 15:17:22 UTC (rev 13283) @@ -1,3 +1,2 @@ -fix_gcc_path fix_usage_name add_hardening Modified: trunk/packages/soap/soapdenovo2/trunk/debian/watch =================================================================== --- trunk/packages/soap/soapdenovo2/trunk/debian/watch 2013-04-09 17:54:02 UTC (rev 13282) +++ trunk/packages/soap/soapdenovo2/trunk/debian/watch 2013-04-10 15:17:22 UTC (rev 13283) @@ -1,5 +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) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
