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<div>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. </div>
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<div>-- </div>
<div><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; ">Dian (Oscar) Jiao, Ph.D.,<br>
Research Associate, Life Sciences Computing Group<br>
Texas Advanced Computing Center<br>
University of Texas at Austin<br>
jiao@tacc.utexas.edu | (832) 303-1166</span></div>
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<span style="font-weight:bold">From: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, October 4, 2012 12:17 PM<br>
<span style="font-weight:bold">To: </span>Oscar Jiao <<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] problem running maker<br>
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<div>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.</div>
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<div>Here are some modules that MAKER can use that I know use C and that you might want to reinstall from CPAN.</div>
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<div>DB_File</div>
<div>Forks</div>
<div>Proc::ProcessTable</div>
<div>Inline::C</div>
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<div>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.</div>
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<div>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.</div>
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<div>Thanks,</div>
<div>Carson</div>
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<span style="font-weight:bold">From: </span>"Dian \"Oscar\" Jiao" <<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 4 October, 2012 11:36 AM<br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] problem running maker<br>
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<div>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.</div>
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<div>-- </div>
<div><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; ">Dian (Oscar) Jiao, Ph.D.,<br>
Research Associate, Life Sciences Computing Group<br>
Texas Advanced Computing Center<br>
University of Texas at Austin<br>
<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a> | (832) 303-1166</span></div>
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<span style="font-weight:bold">From: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, October 4, 2012 9:03 AM<br>
<span style="font-weight:bold">To: </span>Oscar Jiao <<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] problem running maker<br>
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<div>Try 2.26 and let me know.</div>
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<div>Thanks,</div>
<div>Carson</div>
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<span style="font-weight:bold">From: </span>"Dian \"Oscar\" Jiao" <<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 4 October, 2012 10:02 AM<br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] problem running maker<br>
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<div>2.10</div>
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<div>-- </div>
<div><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; ">Dian (Oscar) Jiao, Ph.D.,<br>
Research Associate, Life Sciences Computing Group<br>
Texas Advanced Computing Center<br>
University of Texas at Austin<br>
<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a> | (832) 303-1166</span></div>
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<span style="font-weight:bold">From: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, October 4, 2012 7:27 AM<br>
<span style="font-weight:bold">To: </span>Oscar Jiao <<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] problem running maker<br>
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<div>Are you trying to install 2.26 or 2.10?</div>
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<div>--Carson</div>
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<span style="font-weight:bold">From: </span>"Dian \"Oscar\" Jiao" <<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 4 October, 2012 12:04 AM<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>[maker-devel] problem running maker<br>
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<div style="font-family: Calibri, sans-serif; font-size: 14px; ">Hi, </div>
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<div style="font-family: Calibri, sans-serif; font-size: 14px; ">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</div>
<div style="font-family: Calibri, sans-serif; font-size: 14px; "><br>
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<div style="font-family: Calibri, sans-serif; font-size: 14px; ">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? </div>
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<div style="font-family: Calibri, sans-serif; font-size: 14px; ">Oscar</div>
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