some problems installing velvet

[Yue Xu]

Hi, I have installed velvet, it show some mistakes. Can your help me to find what is wrong with it? Thank you very much.

scaffold.c.text+0x389b): undefined reference to `erf'
scaffold.c.text+0x3b78): undefined reference to `sqrt'
collect2: ld returned 1 exit status
make: *** [color] Error 1

[GenoMax]

Can you post the entire error message?

[Yue Xu]

Thank you for care for this problem. I am sorry. I install velvet in my computer, which is Ok. When My friend who is now at US install it, this error message show. I just can post it in tomorrow.

[Yue Xu]

Can you post the entire error message?

cindylanzao@cindylanzao-NV57H:~/velvet_1.1.05$ make color 'CATEGORIES=57' 'MAXKMERLENGTH=127' 'BIGASSEMBLY=1' 'LONGSEQUENCES=1' 'OPENMP=1'
rm obj/*.o obj/dbg/*.o
rm: cannot remove `obj/dbg/*.o': No such file or directory
make: [cleanobj] Error 1 (ignored)
mkdir -p obj
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/tightString.c -o obj/tightString.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/run.c -o obj/run.o
src/run.c: In function ‘main’:
src/run.c:210:10: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result]
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/splay.c -o obj/splay.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/splayTable.c -o obj/splayTable.o
src/splayTable.c: In function ‘computeClearHSPs’:
src/splayTable.c:591:11: warning: variable ‘start’ set but not used [-Wunused-but-set-variable]
src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’:
src/splayTable.c:929:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/graph.c -o obj/graph.o
src/graph.c: In function ‘addBufferToDescriptor’:
src/graph.c:795:14: warning: variable ‘twinDescr’ set but not used [-Wunused-but-set-variable]
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/run2.c -o obj/run2.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/fibHeap.c -o obj/fibHeap.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/fib.c -o obj/fib.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/concatenatedGraph.c -o obj/concatenatedGraph.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/passageMarker.c -o obj/passageMarker.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/graphStats.c -o obj/graphStats.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/correctedGraph.c -o obj/correctedGraph.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/dfib.c -o obj/dfib.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/dfibHeap.c -o obj/dfibHeap.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/recycleBin.c -o obj/recycleBin.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/readSet.c -o obj/readSet.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/shortReadPairs.c -o obj/shortReadPairs.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o
src/locallyCorrectedGraph.c: In function ‘tourBusNode_local’:
src/locallyCorrectedGraph.c:374:8: warning: variable ‘destination’ set but not used [-Wunused-but-set-variable]
src/locallyCorrectedGraph.c: In function ‘clipTipsVeryHardLocally’:
src/locallyCorrectedGraph.c:421:18: warning: variable ‘twin’ set but not used [-Wunused-but-set-variable]
src/locallyCorrectedGraph.c: In function ‘correctGraphLocally’:
src/locallyCorrectedGraph.c:510:8: warning: variable ‘index’ set but not used [-Wunused-but-set-variable]
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/graphReConstruction.c -o obj/graphReConstruction.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/roadMap.c -o obj/roadMap.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/preGraph.c -o obj/preGraph.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/preGraphConstruction.c -o obj/preGraphConstruction.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/readCoherentGraph.c -o obj/readCoherentGraph.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/utility.c -o obj/utility.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/kmer.c -o obj/kmer.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/scaffold.c -o obj/scaffold.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o
gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=57 -D BIGASSEMBLY -D LONGSEQUENCES -D COLOR -c src/allocArray.c -o obj/allocArray.o
gcc -Wall -fopenmp -O3 -lm -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 -lz
gcc -Wall -fopenmp -O3 -lm -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 -lz
obj/graphStats.o: In function `exportAMOSContigs':
graphStats.c.text+0x3f27): undefined reference to `sqrt'
obj/scaffold.o: In function `estimateMissingInsertLengths':
scaffold.c.text+0x75a): undefined reference to `sqrt'
scaffold.c.text+0x779): undefined reference to `sqrt'
obj/scaffold.o: In function `projectFromReadPair':
scaffold.c.text+0x1eb4): undefined reference to `sqrt'
obj/scaffold.o: In function `buildScaffold':
scaffold.c.text+0x378a): undefined reference to `exp'
scaffold.c.text+0x37b9): undefined reference to `exp'
scaffold.c.text+0x37da): undefined reference to `erf'
scaffold.c.text+0x37fb): undefined reference to `erf'
scaffold.c.text+0x381b): undefined reference to `erf'
scaffold.c.text+0x3848): undefined reference to `exp'
scaffold.c.text+0x387a): undefined reference to `exp'

[GenoMax]

Based on the system prompt above your friend appears to be compiling an older version of velvet. The current version is 1.2.10. That may be worth a try first.

If they want to use the older version for some reason then errors above are pointing to the program not finding the math libraries. Check the Makefile to verify that the following directive is present. If it is not there then add it.

LIBS = -lm

[Yue Xu]

Based on the system prompt above your friend appears to be compiling an older version of velvet. The current version is 1.2.10. That may be worth a try first.

If they want to use the older version for some reason then errors above are pointing to the program not finding the math libraries. Check the Makefile to verify that the following directive is present. If it is not there then add it.

LIBS = -lm

Thank you very much.