Dear Daniel, I forward you a patch from Ubuntu, that reorders parameters passed to ld, in order to build velvet with the --as-needed option of ld. Would you consider it for your next release ?
You can also download the patch from the URL below for more convenience. http://bugs.debian.org/cgi-bin/bugreport.cgi?msg=5;filename=as-needed.patch;att=1;bug=647415 Have a nice day, -- Charles Le Wed, Nov 02, 2011 at 05:27:10PM +0300, Ilya Barygin a écrit : > Package: velvet > Version: 1.1.06~nozlibcopy-1 > Severity: normal > Tags: upstream patch > User: debian-...@lists.debian.org > Usertags: ld-as-needed > > velvet fails to build when --as-needed linker option is enabled, > because of incorrect order of parameters passed to ld. Here's a log of > failed build in Ubuntu: > https://launchpadlibrarian.net/83108674/buildlog_ubuntu-precise-i386.velvet_1.1.06%7Enozlibcopy-1_FAILEDTOBUILD.txt.gz > > See also > http://wiki.debian.org/ToolChain/DSOLinking#Only_link_with_needed_libraries > > The attached patch was used in Ubuntu to fix the problem. > https://launchpad.net/ubuntu/+source/velvet/1.1.06~nozlibcopy-1ubuntu1 > > -- System Information: > Debian Release: wheezy/sid > APT prefers oneiric-updates > APT policy: (500, 'oneiric-updates'), (500, 'oneiric-security'), (500, > 'oneiric-proposed'), (500, 'oneiric'), (100, 'oneiric-backports') > Architecture: i386 (i686) > > Kernel: Linux 3.0.0-13-generic (SMP w/2 CPU cores) > Locale: LANG=ru_RU.UTF-8, LC_CTYPE=ru_RU.UTF-8 (charmap=UTF-8) > Shell: /bin/sh linked to /bin/dash > Description: fix FTBFS with --as-needed linker option > Author: Ilya Barygin <randomact...@ubuntu.com> > > --- velvet-1.1.06~nozlibcopy.orig/Makefile > +++ velvet-1.1.06~nozlibcopy/Makefile > @@ -1,7 +1,7 @@ > CC = gcc > CFLAGS = -Wall > DEBUG = -g > -LDFLAGS = -lm > +LIBS = -lm > OPT = -O3 > MAXKMERLENGTH=31 > CATEGORIES=2 > @@ -67,26 +67,26 @@ clean-zlib : > endif > > 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/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/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/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/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/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/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/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/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 > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". 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