Author: tille Date: 2010-12-20 10:38:44 +0000 (Mon, 20 Dec 2010) New Revision: 5606
Added: trunk/packages/velvet/trunk/debian/patches/ld-as-needed.diff Modified: trunk/packages/velvet/trunk/debian/changelog trunk/packages/velvet/trunk/debian/patches/series trunk/packages/velvet/trunk/debian/rules Log: FIx ld -as-needed FTBFS issue (thanks for the patch to Matthias Klose) Modified: trunk/packages/velvet/trunk/debian/changelog =================================================================== --- trunk/packages/velvet/trunk/debian/changelog 2010-12-20 04:47:29 UTC (rev 5605) +++ trunk/packages/velvet/trunk/debian/changelog 2010-12-20 10:38:44 UTC (rev 5606) @@ -1,3 +1,11 @@ +velvet (1.0.15~nozlibcopy-2) unstable; urgency=low + + * Fix FTBFS with ld --as-needed (thanks for the patch to + Matthias Klose) + Closes: #607535 + + -- Andreas Tille <[email protected]> Mon, 20 Dec 2010 08:43:16 +0100 + velvet (1.0.15~nozlibcopy-1) unstable; urgency=low * New upstream source Added: trunk/packages/velvet/trunk/debian/patches/ld-as-needed.diff =================================================================== --- trunk/packages/velvet/trunk/debian/patches/ld-as-needed.diff (rev 0) +++ trunk/packages/velvet/trunk/debian/patches/ld-as-needed.diff 2010-12-20 10:38:44 UTC (rev 5606) @@ -0,0 +1,53 @@ +Author: Matthias Klose <[email protected]> +Description: Enable ld --as-needed (basically by using LIBS instead of LDFLAGS. + Adding libraries in LDFLAGS is almost always a bad idea. +Closes: #607582 + +Index: velvet-1.0.15~nozlibcopy/Makefile +=================================================================== +--- velvet-1.0.15~nozlibcopy.orig/Makefile 2010-12-19 21:09:32.228228999 +0000 ++++ velvet-1.0.15~nozlibcopy/Makefile 2010-12-19 21:10:14.818229004 +0000 +@@ -1,7 +1,7 @@ + CC = gcc + CFLAGS = -Wall + DEBUG = -g +-LDFLAGS = -lm ++LIBS = -lm + OPT = -O3 + MAXKMERLENGTH=31 + CATEGORIES=2 +@@ -44,26 +44,26 @@ + cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o + + velveth : obj +- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o 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 obj/kmerOccurenceTable.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o 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 obj/kmerOccurenceTable.o $(Z_LIB_FILES) $(LIBS) + + + velvetg : obj +- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.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/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.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/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) $(LIBS) + + debug : override DEF := $(DEF) -D DEBUG + debug : cleanobj obj/dbg +- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) +- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS) + + color : override DEF := $(DEF) -D COLOR + color : cleanobj obj_de +- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de 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 obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) +- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.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/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de 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 obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) $(LIBS) ++ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.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/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) $(LIBS) + + colordebug : override DEF := $(DEF) -D COLOR -D DEBUG + colordebug : cleanobj obj/dbg_de +- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) +- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS) + + objdir: + mkdir -p obj Modified: trunk/packages/velvet/trunk/debian/patches/series =================================================================== --- trunk/packages/velvet/trunk/debian/patches/series 2010-12-20 04:47:29 UTC (rev 5605) +++ trunk/packages/velvet/trunk/debian/patches/series 2010-12-20 10:38:44 UTC (rev 5606) @@ -1,3 +1,4 @@ include_debians_zlib.patch shuffleSequences_fasta.patch fix-perl-path.patch +ld-as-needed.diff Modified: trunk/packages/velvet/trunk/debian/rules =================================================================== --- trunk/packages/velvet/trunk/debian/rules 2010-12-20 04:47:29 UTC (rev 5605) +++ trunk/packages/velvet/trunk/debian/rules 2010-12-20 10:38:44 UTC (rev 5606) @@ -14,10 +14,10 @@ pkg=velvet -DEB_MAKE_BUILD_TARGET = obj velveth velvetg Z_LIB_FILES='' LDFLAGS='-lm -lz' OPT='' +DEB_MAKE_BUILD_TARGET = obj velveth velvetg Z_LIB_FILES='' LIBS='-lm -lz' OPT='' build/velvet:: - make color CFLAGS='$(CFLAGS)' Z_LIB_FILES='' LDFLAGS='-lm -lz' OPT='' + make color CFLAGS='$(CFLAGS)' Z_LIB_FILES='' LIBS='-lm -lz' OPT='' mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/ help2man --no-info --name="simple hashing program" \ $(CURDIR)/velveth > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/velveth.1 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
