Error In Velvet 1.2.10 Installation In Debian
2
0
Entering edit mode
11.3 years ago
sentausa ▴ 650

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?

velvet installation • 4.8k views
ADD COMMENT
2
Entering edit mode
11.3 years ago
JC 13k

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

apt-get install velvet

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode
11.3 years ago
cts ★ 1.7k

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

ADD COMMENT
0
Entering edit mode

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).

ADD REPLY

Login before adding your answer.

Traffic: 1848 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6