Question: Error In Velvet 1.2.10 Installation in Kubuntu
0
gravatar for chariko
4.8 years ago by
chariko30
Spain
chariko30 wrote:

Hi all,

As user sentausa in his post:

A: 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?

velvet 1.2.10 installation • 2.0k views
ADD COMMENTlink modified 3.8 years ago by Biostar ♦♦ 20 • written 4.8 years ago by chariko30

Quick question: Why sudo make and not just make?

ADD REPLYlink written 4.8 years ago by RamRS20k

if i do just make I get the same error. 

ADD REPLYlink written 4.8 years ago by chariko30

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

ADD REPLYlink written 4.8 years ago by RamRS20k

Hi,

Did the solution I suggested help at all?

ADD REPLYlink written 4.8 years ago by RamRS20k
1
gravatar for RamRS
4.8 years ago by
RamRS20k
Houston, TX
RamRS20k wrote:

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

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by RamRS20k
0
gravatar for chariko
4.8 years ago by
chariko30
Spain
chariko30 wrote:

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.

 

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by chariko30

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

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Antonio R. Franco4.0k

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

ADD REPLYlink written 3.8 years ago by Adrian Pelin2.2k
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