Question: Error In Velvet 1.2.10 Installation In Debian
0
gravatar for sentausa
5.7 years ago by
sentausa630
France
sentausa630 wrote:

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?

installation velvet • 3.1k views
ADD COMMENTlink modified 5.7 years ago by cts1.6k • written 5.7 years ago by sentausa630
2
gravatar for JC
5.7 years ago by
JC7.7k
Mexico
JC7.7k wrote:

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

apt-get install velvet

ADD COMMENTlink written 5.7 years ago by JC7.7k

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 REPLYlink written 5.7 years ago by matted7.0k

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 REPLYlink written 5.6 years ago by sentausa630
1
gravatar for cts
5.7 years ago by
cts1.6k
Pasadena
cts1.6k wrote:

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 COMMENTlink written 5.7 years ago by cts1.6k

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 REPLYlink written 5.6 years ago by sentausa630
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