Error In Velvet 1.2.10 Installation In Debian

Question

[sentausa]

Hi all. I wanted to install velvet 1.2.10 to make an assembly from MiSeq paired-end fastq files. In my VirtualBox Debian, after 'tar -xzvf velvet_1.2.10.tgz', I 'make' as root. And it showed this error:

root@debian:/home/user/Downloads/velvet_1.2.10# make
rm obj/*.o obj/dbg/*.o 
rm: cannot remove `obj/*.o': No such file or directory
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 
src/graphStats.c: In function ‘collectReferenceCoords’:
src/graphStats.c:1961: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘long long int’
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:38:18: error: zlib.h: No such file or directory
src/readSet.c: In function ‘readRawGZFile’:
src/readSet.c:459: error: ‘gzFile’ undeclared (first use in this function)
src/readSet.c:459: error: (Each undeclared identifier is reported only once
src/readSet.c:459: error: for each function it appears in.)
src/readSet.c:459: error: expected ‘;’ before ‘file’
src/readSet.c:466: error: ‘file’ undeclared (first use in this function)
src/readSet.c:466: warning: implicit declaration of function ‘gzopen’
src/readSet.c:468: warning: implicit declaration of function ‘gzdopen’
src/readSet.c:477: warning: implicit declaration of function ‘gzgets’
src/readSet.c:490: warning: implicit declaration of function ‘gzclose’
src/readSet.c: At top level:
src/readSet.c:555: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘openFastXFile’
src/readSet.c:602: error: expected specifier-qualifier-list before ‘gzFile’
src/readSet.c: In function ‘fileGZOrAuto_read’:
src/readSet.c:608: error: ‘FileGZOrAuto’ has no member named ‘gzFile’
src/readSet.c:609: warning: implicit declaration of function ‘gzread’
src/readSet.c:609: error: ‘FileGZOrAuto’ has no member named ‘gzFile’
src/readSet.c:611: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c: In function ‘fileGZOrAuto_close’:
src/readSet.c:616: error: ‘FileGZOrAuto’ has no member named ‘gzFile’
src/readSet.c:617: error: ‘FileGZOrAuto’ has no member named ‘gzFile’
src/readSet.c:619: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c: In function ‘readFastXFile’:
src/readSet.c:641: error: ‘FileGZOrAuto’ has no member named ‘gzFile’
src/readSet.c:641: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c:643: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c:644: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c:646: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c:646: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c:648: error: ‘FileGZOrAuto’ has no member named ‘gzFile’
src/readSet.c:648: warning: implicit declaration of function ‘openFastXFile’
src/readSet.c: In function ‘readFastXPair’:
src/readSet.c:680: error: ‘FileGZOrAuto’ has no member named ‘gzFile’
src/readSet.c:680: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c:681: error: ‘FileGZOrAuto’ has no member named ‘gzFile’
src/readSet.c:681: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c:683: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c:684: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c:686: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c:686: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c:687: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c:688: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c:690: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c:690: error: ‘FileGZOrAuto’ has no member named ‘autoFile’
src/readSet.c:692: error: ‘FileGZOrAuto’ has no member named ‘gzFile’
src/readSet.c:693: error: ‘FileGZOrAuto’ has no member named ‘gzFile’
src/readSet.c: At top level:
src/readSet.c:945: error: expected ‘)’ before ‘file’
src/readSet.c: In function ‘readBAMFile’:
src/readSet.c:964: error: ‘gzFile’ undeclared (first use in this function)
src/readSet.c:964: error: expected ‘;’ before ‘file’
src/readSet.c:991: error: ‘file’ undeclared (first use in this function)
src/readSet.c:1006: warning: implicit declaration of function ‘gzseek’
src/readSet.c:1006: warning: implicit declaration of function ‘readBAMint32’
make: *** [obj/readSet.o] Error 1

I don't understand what happened and it seems that velvet's current online manual doesn't really help with installation. Anybody can help me please?

Answer 1

[JC]

You have missing the Zlib source, try to install de devel version or install the binary from the repos:

apt-get install velvet

[matted]

You can install the zlib headers and library with sudo apt-get install zlib1g-dev on Ubuntu. Not sure of the exact Debian package name.

[sentausa]

I tried apt-get install velvet before, but I believe the installed version is not 1.2 since it cannot use the -separate option for my paired-end dataset.

Answer 2

[cts]

I agree with JC about not having Zlib installed, but velvet comes bundled with it so you don't need to install it separately. When installing velvet type make 'BUNDLEDZLIB=1' to using the zlib that is packaged with velvet. There are other options as well that you could find handy, which are listed in the velvet manual

[sentausa]

Thank you, now there's no error after 'make'. So in fact it was mentioned in the manual, after all (though I supposed it's meant only for more experienced Linux user, unlike me :p).