[maker-devel] problem running maker

[David Powell]

I've also had the problem with a segfault when running MAKER 2.26.  I'm not
sure it is the one experienced here, but in the end I was able to work
around it.

I tracked the problem to lib/FastA.pm in the _safe_new function.
 Specifically, in the local handler installed for warnings.  By removing
the "die" call, I was able to stop the perl process from segfaulting.  I
suspect this is not a great fix since it will ignore any warnings from
Bio::DB::Fasta, but it worked for me (I did check the warnings generated
were not important).

Cheers,

-- David Powell


On 5 October 2012 03:17, Carson Holt <carsonhh at gmail.com> wrote:

> 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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