Hello Charles,
Sure thing, I'll commit it shortly.
Regards,
Daniel
On 02/11/2011 17:56, Charles Plessy wrote:
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
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