Error In Velvet 1.2.10 Installation in Kubuntu

Question

[chariko]

Hi all,

As user sentausa in his post:

Error In Velvet 1.2.10 Installation In Debian

I have the same problem when trying to install velvet 1.2.10 in Kubuntu. I tar the file and when doing "make" as root I get a similar error:

chariko@NGS:~/Illumina/software/velvet_1.2.10$ sudo make velveth velvetg

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 -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o 
In file included from <command-line>:0:0:
/usr/include/stdc-predef.h:30:26: fatal error: bits/predefs.h: No such file or directory
 #include <bits/predefs.h>
                          ^
compilation terminated.
make: *** [obj/tightString.o] Error 1

I tried also make BUNDLEDZLIB=1:

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)
cd third-party/zlib-1.2.3; ./configure; make; rm minigzip.o; rm example.o
Checking for gcc...
Building static library libz.a version 1.2.3 with gcc.
Checking for unistd.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf()
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
Checking for errno.h... Yes.
Checking for mmap support... Yes.
make[1]: Entering directory `/home/chariko/Illumina/software/velvet_1.2.10/third-party/zlib-1.2.3'
gcc -O3 -DUSE_MMAP   -c -o example.o example.c
gcc -O3 -DUSE_MMAP   -c -o adler32.o adler32.c
gcc -O3 -DUSE_MMAP   -c -o compress.o compress.c
gcc -O3 -DUSE_MMAP   -c -o crc32.o crc32.c
gcc -O3 -DUSE_MMAP   -c -o gzio.o gzio.c
gcc -O3 -DUSE_MMAP   -c -o uncompr.o uncompr.c
gcc -O3 -DUSE_MMAP   -c -o deflate.o deflate.c
gcc -O3 -DUSE_MMAP   -c -o trees.o trees.c
gcc -O3 -DUSE_MMAP   -c -o zutil.o zutil.c
gcc -O3 -DUSE_MMAP   -c -o inflate.o inflate.c
gcc -O3 -DUSE_MMAP   -c -o infback.o infback.c
gcc -O3 -DUSE_MMAP   -c -o inftrees.o inftrees.c
gcc -O3 -DUSE_MMAP   -c -o inffast.o inffast.c
ar rc libz.a adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o zutil.o inflate.o infback.o inftrees.o inffast.o 
gcc -O3 -DUSE_MMAP -o example example.o -L. libz.a
gcc -O3 -DUSE_MMAP   -c -o minigzip.o minigzip.c
gcc -O3 -DUSE_MMAP -o minigzip minigzip.o -L. libz.a
make[1]: Leaving directory `/home/chariko/Illumina/software/velvet_1.2.10/third-party/zlib-1.2.3'
mkdir -p obj
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/tightString.c -o obj/tightString.o 
In file included from <command-line>:0:0:
/usr/include/stdc-predef.h:30:26: fatal error: bits/predefs.h: No such file or directory
 #include <bits/predefs.h>
                          ^
compilation terminated.
make: *** [obj/tightString.o] Error 1

and also got the same error. Can anyone help me?

[Ram]

Quick question: Why sudo make and not just make?

[chariko]

if I do just make I get the same error.

[Ram]

Either the make file is faulty (highly improbable) or I am overlooking something really simple

[Ram]

Hi,

Did the solution I suggested help at all?

Answer 1

[Ram]

Did some Googling, the error may be because you need 32 bit libraries for predefs.h.

Try running

sudo apt-get install libc6-dev-i386

Then

make

Answer 2

[chariko]

I tried to install the package by downloading it from the web (muon did not find it) and I got the following error:

dpkg: error processing libc6-dev-i386_2.17-93ubuntu4_amd64.deb (--install):
 package architecture (amd64) does not match system (i386)
Errors were encountered while processing:
 libc6-dev-i386_2.17-93ubuntu4_amd64.deb

That means that I have installed a 32bit version of Kubuntu and the package I downloaded is for amd64. I tried to look for a 32 bit version of the package and it was not available so finally I was not able to install the package you recommended.

[Antonio R. Franco]

An assembler like velvet will generate a lot of memory resources at the time of generating and manipulating the Der Bruijn graphs.

You can handle a little bit less than 4Gb of RAM memory with a 32bit system, so in most cases, it has not sense to compile velvet in a 32bit mode

[Adrian Pelin]

Apparently this is an 11 month old post, but for some reason it got bumped by Biostars....