Question: Trouble with installation Trinity on Linux 32 bit
0
gravatar for seta
2.6 years ago by
seta1.2k
Sweden
seta1.2k wrote:

Hi all,

I'm trying to install Trinity on Ubuntu 13.10, 32 bit, but I faced with the following error:

Using gnu compiler for Inchworm and Chrysalis
cd Inchworm && (test -e configure || autoreconf) \
            && ./configure --prefix=`pwd`  && make install
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for library containing cos... none required
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
make[1]: Entering directory `/home/dps/trinityrnaseq_r20140717/Inchworm'
Making install in src
make[2]: Entering directory `/home/dps/trinityrnaseq_r20140717/Inchworm/src'
if g++ -DHAVE_CONFIG_H -I. -I. -I..    -pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated -m64 -g -O2 -MT Fasta_entry.o -MD -MP -MF  ".deps/Fasta_entry.Tpo" -c -o Fasta_entry.o Fasta_entry.cpp; \
then mv -f ".deps/Fasta_entry.Tpo" ".deps/Fasta_entry.Po"; else rm -f ".deps/Fasta_entry.Tpo"; exit 1; fi
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[2]: *** [Fasta_entry.o] Error 1
make[2]: Leaving directory `/home/dps/trinityrnaseq_r20140717/Inchworm/src'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/dps/trinityrnaseq_r20140717/Inchworm'
make: *** [inchworm_target] Error 2

I tried to solve the problem with the following commands as I found on the net:

sudo apt-get install build-essential
sudo apt-get install libc6-dev-i386
sudo apt-get install libc6-dev
sudo apt-get install g++-4.8-multilib

But, unfortunately, none of the commands execute well. Could you please help me out to solve the problem?

Thank you in advance

ADD COMMENTlink modified 2.6 years ago by Farbod3.3k • written 2.6 years ago by seta1.2k
1

maybe this helps: http://stackoverflow.com/questions/12591629/gcc-cannot-find-bits-predefs-h-on-i686

ADD REPLYlink written 2.6 years ago by bzg40

Trinity is resource-intensive... I suspect installing it on a 32-bit OS would be a waste of time.

ADD REPLYlink written 2.6 years ago by Brian Bushnell16k

You're completely right, Brian. The purpose is just training and working with very small data; however, now, I'm curious what is the problem?

ADD REPLYlink written 2.6 years ago by seta1.2k

Hmm. So you also decided to use 32-bit OS. Is that because you are using VM's with meager specs? If not this choice does not make sense.

ADD REPLYlink written 2.6 years ago by genomax69k

As of today, most processors and cloud providers offer the possibility to run 64-bit systems. If you can install a recent 64-bit Ubuntu, then you can also install directly Trinity via the packaging system. Then you can focus on training on your small dataset (unless of course you are also interested to train in compiling software).

$ rmadison trinityrnaseq -uubuntu
 trinityrnaseq | 2.2.0+dfsg-2 | yakkety/universe | source, amd64
 trinityrnaseq | 2.2.0+dfsg-2 | zesty/universe   | source, amd64
ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Charles Plessy2.7k
1
gravatar for Farbod
2.6 years ago by
Farbod3.3k
Toronto
Farbod3.3k wrote:

Dear seta, Hi

It seems that it is not possible to run Trinity on 32 bit Linux, even on small data set.

~ Best

ADD COMMENTlink written 2.6 years ago by Farbod3.3k
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