[maker-devel] problem running maker

[Dian "Oscar" Jiao]

I tried the debug trick and it worked (at least it finished). I however when I looked at the stderr, I again noticed the "can't locate GDBM_File for @AnyDBM_File::ISA" error. Although it did not affect the output, is it what is causing the segmentation error? Because this is the only error other than a bunch of "UNKOWN Bio" messages.
--
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<mailto:carsonhh at gmail.com>>
Date: Thursday, October 4, 2012 12:17 PM
To: Oscar Jiao <jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] problem running maker

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<mailto:jiao at tacc.utexas.edu>>
Date: Thursday, 4 October, 2012 11:36 AM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto: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<mailto:jiao at tacc.utexas.edu> | (832) 303-1166

From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Thursday, October 4, 2012 9:03 AM
To: Oscar Jiao <jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto: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<mailto:jiao at tacc.utexas.edu>>
Date: Thursday, 4 October, 2012 10:02 AM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto: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<mailto:jiao at tacc.utexas.edu> | (832) 303-1166

From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Thursday, October 4, 2012 7:27 AM
To: Oscar Jiao <jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto: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<mailto:jiao at tacc.utexas.edu>>
Date: Thursday, 4 October, 2012 12:04 AM
To: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto: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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