Author: tille Date: 2011-04-15 08:56:06 +0000 (Fri, 15 Apr 2011) New Revision: 6573
Removed: trunk/packages/velvet/trunk/debian/patches/meta-velvet.patch Modified: trunk/packages/velvet/trunk/debian/README.source trunk/packages/velvet/trunk/debian/changelog trunk/packages/velvet/trunk/debian/get-orig-source trunk/packages/velvet/trunk/debian/patches/series Log: Once we are rebuilding the original tarball anyway, it seems simpler to remove the outdated MetaVelvet code rather than adapting the build system. If MetaVelvet is needed it should be packaged separately. The issue is documented in README.source. Modified: trunk/packages/velvet/trunk/debian/README.source =================================================================== --- trunk/packages/velvet/trunk/debian/README.source 2011-04-15 07:37:10 UTC (rev 6572) +++ trunk/packages/velvet/trunk/debian/README.source 2011-04-15 08:56:06 UTC (rev 6573) @@ -9,7 +9,17 @@ -- Charles Plessy <ple...@debian.org> Mon, 25 Jan 2010 13:03:06 +0900 +Since version 1.0.2 of velvet the source tarball contains an extra copy +of a velvet extension called MetaVelvet. There is a lot of duplicated +code which was removed from the tarball to simplify the build system of +the Debian package. The latest version of MetaVelvet can always be +downloaded here: + https://github.com/hacchy/MetaVelvet + + -- Andreas Tille <ti...@debian.org> Fri, 15 Apr 2011 10:51:16 +0200 + + This package uses a patch system. ───────────────────────────────── Modified: trunk/packages/velvet/trunk/debian/changelog =================================================================== --- trunk/packages/velvet/trunk/debian/changelog 2011-04-15 07:37:10 UTC (rev 6572) +++ trunk/packages/velvet/trunk/debian/changelog 2011-04-15 08:56:06 UTC (rev 6573) @@ -6,10 +6,12 @@ changes * Debhelper 8 (control+compat) * debian/rules: Leave out Z_LIB_FILES in parameter list - * debian/patches/meta-velvet.patch: Enable building meta-velvet - in contrib + * debian/get-orig-source: Once we are rebuilding the original + tarball anyway it makes sense to remove an outdated copy of + MetaVelvet and replace it rather by a hint to the currently + maintained source in README.source - -- Andreas Tille <ti...@debian.org> Tue, 05 Apr 2011 14:18:24 +0200 + -- Andreas Tille <ti...@debian.org> Fri, 15 Apr 2011 10:51:16 +0200 velvet (1.0.18~nozlibcopy-1) unstable; urgency=low Modified: trunk/packages/velvet/trunk/debian/get-orig-source =================================================================== --- trunk/packages/velvet/trunk/debian/get-orig-source 2011-04-15 07:37:10 UTC (rev 6572) +++ trunk/packages/velvet/trunk/debian/get-orig-source 2011-04-15 08:56:06 UTC (rev 6573) @@ -23,6 +23,10 @@ # delete .DS_Store files find ${UPSTREAMDIR} -name .DS_Store -exec rm -f \{\} \; +# remove separate project which is basically a duplication of velvet code +# this should be packaged separately with an up to date version +rm -rf ${UPSTREAMDIR}/contrib/MetaVelvet* + mv ${UPSTREAMDIR} ${UPSTREAMDIR}~nozlibcopy GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION~nozlibcopy".orig.tar.gz "${UPSTREAMDIR}~nozlibcopy" Deleted: trunk/packages/velvet/trunk/debian/patches/meta-velvet.patch =================================================================== --- trunk/packages/velvet/trunk/debian/patches/meta-velvet.patch 2011-04-15 07:37:10 UTC (rev 6572) +++ trunk/packages/velvet/trunk/debian/patches/meta-velvet.patch 2011-04-15 08:56:06 UTC (rev 6573) @@ -1,50 +0,0 @@ ---- velvet_1.1.02~nozlibcopy.orig/contrib/MetaVelvet-v0.3.1/Makefile -+++ velvet_1.1.02~nozlibcopy/contrib/MetaVelvet-v0.3.1/Makefile -@@ -1,14 +1,15 @@ - CC = gcc - CFLAGS = -Wall - DEBUG = -g --LDFLAGS = -lm -+LIBS = -lm - OPT = -O3 - MAXKMERLENGTH=31 - CATEGORIES=2 - DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES) - - Z_LIB_DIR=../../third-party/zlib-1.2.3 --Z_LIB_FILES=$(Z_LIB_DIR)/*.o -+# In Debian we do not use local zlib copy, however, we need to add $(LIBS) to compile options and thus we tweak this in here: -+Z_LIB_FILES=$(LIBS) - - # Mac OS users: uncomment the following lines - # Z_LIB_FILES= -@@ -21,7 +22,7 @@ - OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/crc.o obj/utility.o obj/kmer.o obj/scaffold.o - OBJDBG = $(subst obj,obj/dbg,$(OBJ)) - --default : cleanobj zlib obj meta-velveth meta-velvetg -+default : cleanobj obj meta-velveth meta-velvetg - - clean : - -rm obj/*.o obj/dbg/*.o ./meta-velvet* -@@ -31,7 +32,8 @@ - -rm obj/*.o obj/dbg/*.o - - zlib : -- cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o -+ # cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o -+ echo "Use Debian packaged version of zlib" - - meta-velveth : obj - $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o meta-velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(Z_LIB_FILES) ---- velvet_1.1.02~nozlibcopy.orig/contrib/MetaVelvet-v0.3.1/src/readSet.c -+++ velvet_1.1.02~nozlibcopy/contrib/MetaVelvet-v0.3.1/src/readSet.c -@@ -32,7 +32,7 @@ - #if defined(_WIN32) || defined(__WIN32__) || defined(WIN32) - #include "../third-party/zlib-1.2.3/Win32/include/zlib.h" - #else --#include "../third-party/zlib-1.2.3/zlib.h" -+#include <zlib.h> - #endif - - #if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__) Modified: trunk/packages/velvet/trunk/debian/patches/series =================================================================== --- trunk/packages/velvet/trunk/debian/patches/series 2011-04-15 07:37:10 UTC (rev 6572) +++ trunk/packages/velvet/trunk/debian/patches/series 2011-04-15 08:56:06 UTC (rev 6573) @@ -2,4 +2,3 @@ shuffleSequences_fasta.patch fix-perl-path.patch ld-as-needed.patch -meta-velvet.patch _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
