[maker-devel] problem running maker

[Carson Holt]

Seg faults really only happen from C and not Perl, so there may be a perl
module that is broken on your machine that use C internally.

Here are some modules that MAKER can use that I know use C and that you
might want to reinstall from CPAN.

DB_File
Forks
Proc::ProcessTable
Inline::C

Also during the maker install say no to the "use MPI" question.  It's best
to make the installation as simple as possible before getting into MPI
configuration.

Also after installing those and rerunning maker's 'perl Build.PL' and
'./Build install' steps do your first run with 'maker --debug' (redirect
STDERR to a file).  Then if it fails, you can send me the error log.

Thanks,
Carson


From:  "Dian \"Oscar\" Jiao" <jiao at tacc.utexas.edu>
Date:  Thursday, 4 October, 2012 11:36 AM
To:  Carson Holt <carsonhh at gmail.com>, "maker-devel at yandell-lab.org"
<maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] problem running maker

Ok. So I installed 2.26 instead. When I ran maker again I got segmentation
fault with no additional message. I am using dpp_contig.fasta, dpp_est.fasta
and dpp_protein.fasta.

-- 
Dian (Oscar) Jiao, Ph.D.,
Research Associate, Life Sciences Computing Group
Texas Advanced Computing Center
University of Texas at Austin
jiao at tacc.utexas.edu | (832) 303-1166

From: Carson Holt <carsonhh at gmail.com>
Date: Thursday, October 4, 2012 9:03 AM
To: Oscar Jiao <jiao at tacc.utexas.edu>, "maker-devel at yandell-lab.org"
<maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] problem running maker

Try 2.26 and let me know.

Thanks,
Carson

From: "Dian \"Oscar\" Jiao" <jiao at tacc.utexas.edu>
Date: Thursday, 4 October, 2012 10:02 AM
To: Carson Holt <carsonhh at gmail.com>, "maker-devel at yandell-lab.org"
<maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] problem running maker

2.10
-- 
Dian (Oscar) Jiao, Ph.D.,
Research Associate, Life Sciences Computing Group
Texas Advanced Computing Center
University of Texas at Austin
jiao at tacc.utexas.edu | (832) 303-1166

From: Carson Holt <carsonhh at gmail.com>
Date: Thursday, October 4, 2012 7:27 AM
To: Oscar Jiao <jiao at tacc.utexas.edu>, "maker-devel at yandell-lab.org"
<maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] problem running maker

Are you trying to install 2.26 or 2.10?

--Carson


From: "Dian \"Oscar\" Jiao" <jiao at tacc.utexas.edu>
Date: Thursday, 4 October, 2012 12:04 AM
To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: [maker-devel] problem running maker

Hi, 

I just installed maker and tried to run it with these dpp example fasta
files that came with the package. However when I do "maker maker_opts.ctl
maker_bopts.ctl maker_exe.ctl", I got the following errors. It looks like
there are three errors: (1) defined array deprecated; (2) unknown state in
Signal.pm and (3) GDBM_File (etc.) missing

The first line seems to be just warning. I got it even when I do just
"maker" or "maker ctl". The control files did get generated. And what is the
relationship between the three perl modules, GDBM/NDBM/SDBM_File, AnyDBM and
DB_File? 

Oscar

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