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  • Velvet compilation: basic question

    Hi all,

    Hopefully a quick question.

    I am quite a beginner in linux, but willing to learn! I have ubuntu and use it regularly for mundane things that are installable via their graphical interface. When it comes to installing manually and compiling, I am often clueless when an error pops up.

    I have trouble installing velvet (log below). Could someone advise me on what I should do? The log below is what I get when I type "make" in the velvet unzipped install files directory.

    Thank you very much for your help.

    GM


    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 
    src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’:
    src/splayTable.c:1060:14: warning: variable ‘refElem’ set but not used [-Wunused-but-set-variable]
    src/splayTable.c:1206:11: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
    src/splayTable.c:1212:11: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
    src/splayTable.c: In function ‘scanBinaryReferenceSequences’:
    src/splayTable.c:933:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
    src/splayTable.c:949:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
    src/splayTable.c: In function ‘scanReferenceSequences’:
    src/splayTable.c:877:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
    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 
    src/readSet.c:37:18: fatal error: zlib.h: No such file or directory
    compilation terminated.
    make: *** [obj/readSet.o] Error 1

  • #2
    You need to install the "zlib" package. You should be able to do it through Ubuntu package manager.

    This is a link from a google search to do this on command line: http://kobablog.wordpress.com/2011/0...ile-in-ubuntu/

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