Dear all,
The Velvet (v 1.2.06) "make" returns an error when I try to install it on my server (CentOS 5.7). Could someone help me solve the problem? I would really appreciate it.
The Velvet (v 1.2.06) "make" returns an error when I try to install it on my server (CentOS 5.7). Could someone help me solve the problem? I would really appreciate it.
Code:
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 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o gcc -Wall -O3 -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o -lz -lm obj/readSet.o: In function `openFastXFile': readSet.c:(.text+0x824): undefined reference to `gzgetc_' collect2: ld returned 1 exit status make: *** [velveth] Error 1
Comment