help with Trinity installation

[cli]

Dear all,

We want to install Trinity on our cluster, which is under x86_64-redhat-linux, Thread model: posix, gcc version 4.1.2 20080704 (Red Hat 4.1.2-50). When I tried to compile Trinity, I got errors:

Use of inherited AUTOLOAD for non-method Autom4te::XFile::msg() is deprecated at /usr/share/autoconf/Autom4te/XFile.pm line 238.
Can't locate auto/Autom4te/XFile/msg.al in @INC (@INC contains: /usr/share/autoconf /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/share/autoconf/Autom4te/XFile.pm line 238
aclocal-1.9: autom4te failed with exit status: 1
make[1]: *** [aclocal.m4] Error 1
make[1]: Leaving directory `/ocean/rhome/lichenhong/trinityrnaseq_r20140413p1/Inchworm'
make: *** [inchworm_target] Error 2

Does anyone know what was the problem and how to fix it? Or if you have compiled executables that we could use, it would be greatly appreciated. We really need the cluster to do the job in time. Thank you in advance.

[WhatsOEver]

Something like:

Can't locate auto/Autom4te/XFile/msg.al in @INC...

normally tells you that some perl libraries are missing/cannot be found.
I found a similar (but quite old) bug report on this (https://bugzilla.redhat.com/show_bug.cgi?id=494042) with a possible fix by adding: "use Autom4te::Channels qw(msg);" to .../lib/Autom4te/XFile.pm.

It seems to be a problem specific to installations on a server/cluster; At least I haven't had this error when I installed trinity 2 weeks ago on a local workstation.

Hope this helps somehow.

[cli]

Thank you, WhatsOEver!

We have fixed the problem by point the compiler to gcc 44. Since we can't mess with the root system, here are what we did. Hope it can help someone facing similar problem.

1. adding alias 'gcc=/usr/bin/gcc44' alias 'g++=/usr/bin/g++44' in .bashrc file

2. modify the jellyfish plugin / Makefile, find jellyfish configure=XXX and change it into configure=usr/bin/gcc44

[kurban910]

error with trinity installation

hello everyone,

i have rent server from school computer center, and trying to install Trinity on it via SSH. but i got the following error message:

kurban910@node9:~/trinityrnaseq-2.0.6> make
Using gnu compiler for Inchworm and Chrysalis
cd Inchworm && (test -e configure || autoreconf) \
                && sh ./configure --prefix=`pwd`  && make install
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
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 `/public/home/kurban910/trinityrnaseq-2.0.6/Inchworm'
make[1]: Warning: File `Makefile' has modification time 5e+04 s in the future
Making install in src
make[2]: Entering directory `/public/home/kurban910/trinityrnaseq-2.0.6/Inchworm/src'
make[2]: Warning: File `.deps/string_util.Po' has modification time 4.9e+04 s in the future
g++ -DHAVE_CONFIG_H -I. -I..    -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT Fasta_entry.o -MD -MP -MF .deps/Fasta_entry.Tpo -c -o Fasta_entry.o Fasta_entry.cpp
cc1plus: error: unrecognized command line option "-std=c++0x"
cc1plus: error: unrecognized command line option "-fopenmp"
make[2]: *** [Fasta_entry.o] Error 1
make[2]: Leaving directory `/public/home/kurban910/trinityrnaseq-2.0.6/Inchworm/src'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/public/home/kurban910/trinityrnaseq-2.0.6/Inchworm'
make: *** [inchworm_target] Error 2
kurban910@node9:~/trinityrnaseq-2.0.6>

i am still new at linux operation. could anyone give me some sugessions what have gone wrong here?

[GenoMax]

Which version of gcc are you using?

$ gcc -v

[kurban910]

kurban910@node9:~/trinityrnaseq-2.0.6> gcc -v
Using built-in specs.
Target: x86_64-suse-linux
Configured with: ../configure --enable-threads=posix --prefix=/usr --with-local-prefix=/usr/local --infodir=/usr/share/info --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-languages=c,c++,objc,fortran,obj-c++,java,ada --enable-checking=release --with-gxx-include-dir=/usr/include/c++/4.1.2 --enable-ssp --disable-libssp --disable-libgcj --with-slibdir=/lib64 --with-system-zlib --enable-shared --enable-__cxa_atexit --enable-libstdcxx-allocator=new --program-suffix= --enable-version-specific-runtime-libs --without-system-libunwind --with-cpu=generic --host=x86_64-suse-linux
Thread model: posix
gcc version 4.1.2 20070115 (SUSE Linux)

[GenoMax]

That is a pretty old version of gcc. You will need a new(er) version of gcc to compile trinity. Ask your admins if gcc (v. 4.3 or newer) is available.

[kurban910]

thanks GenoMax,
is there anyway can i update gcc without contacting with the people who is responsible for the server? coz, it's time for off-work here in uqumqi. if i wait untill tomorrow i will wait like another 15 hours.

[GenoMax]

You won't be able to update system gcc (only admins can do that). It appears that you are using SUSE linux (is this openSUSE or something else?).

[kurban910]

kurban910@node9:~/trinityrnaseq-2.0.6> cat /proc/version
Linux version 2.6.16.60-0.21-smp (geeko@buildhost) (gcc version 4.1.2 20070115 (SUSE Linux)) #1 SMP Tue May 6 12:41:02 UTC 2008
kurban910@node9:~/trinityrnaseq-2.0.6> lsb_release-a
-bash: lsb_release-a: command not found
kurban910@node9:~/trinityrnaseq-2.0.6> cat /etc/issue

Welcome to SUSE Linux Enterprise Server 10 SP2 (x86_64) - Kernel \r (\l).


kurban910@node9:~/trinityrnaseq-2.0.6>

from the info. above can we know its open suse or not ?

[GenoMax]

Sorry I have not worked with SUSE so can't give you specific directions on how to get a newer version of gcc installed. See if something here works: https://forums.opensuse.org/showthre...g-gcc-compiler

[kurban910]

thanks , i will look into that.

[andrewm]

In case this is still an issue for anyone, its possible the problem is the filesystem you are compiling on.

Try a local filesystem as opposed to an NFS mount.

https://bugzilla.redhat.com/show_bug.cgi?id=494042

[gen2prot]

Help with trinity installation

Hello,

I followed the instructions on installing Trinity. I gave the following commands

make
make plugins

It works fine upto here. When I give the next command,

make install

I get an error as I do not have permission to write to /usr/local/bin, as it is owned by "root"

How do I solve this?

I have tried the following, all getting errors

make prefix=/path/to/installationdir install
make -C /path/to/installationdir install

Thanks in advance
-Abhijit

[yueluo]

You don't need to run 'make install' for Trinity to work. Just execute /path/to/Trinity .