<div><br></div><div>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. </div><div><br></div><div>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).</div>
<div><br></div><div>Cheers,</div><div><br></div><div>-- David Powell</div><div><br></div><div><br></div>On 5 October 2012 03:17, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br>
<div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><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>
<div><br></div><div>Here are some modules that MAKER can use that I know use C and that you might want to reinstall from CPAN.</div><div><br></div><div>DB_File</div><div>Forks</div><div>Proc::ProcessTable</div><div>Inline::C</div>
<div><br></div><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><div><br></div><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>
<div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<div class="im"><span style="font-weight:bold">From: </span> "Dian \"Oscar\" Jiao" <<a href="mailto:jiao@tacc.utexas.edu" target="_blank">jiao@tacc.utexas.edu</a>><br></div><span style="font-weight:bold">Date: </span> Thursday, 4 October, 2012 11:36 AM<div>
<div class="h5"><br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>>, "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span> Re: [maker-devel] problem running maker<br></div></div></div><div><div class="h5"><div><br></div><div><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div><div><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><div><br></div><div><div><div>
-- </div><div><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" target="_blank">jiao@tacc.utexas.edu</a> | <a href="tel:%28832%29%20303-1166" value="+18323031166" target="_blank">(832) 303-1166</a></span></div></div></div></div></div><div><br></div>
<span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">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" target="_blank">jiao@tacc.utexas.edu</a>>, "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] problem running maker<br></div><div><br></div><div><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>Try 2.26 and let me know.</div>
<div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span>"Dian \"Oscar\" Jiao" <<a href="mailto:jiao@tacc.utexas.edu" target="_blank">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" target="_blank">carsonhh@gmail.com</a>>, "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] problem running maker<br></div><div><br></div><div><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div><div><div>2.10</div>
<div><div><div>-- </div><div><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" target="_blank">jiao@tacc.utexas.edu</a> | <a href="tel:%28832%29%20303-1166" value="+18323031166" target="_blank">(832) 303-1166</a></span></div></div>
</div></div></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">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" target="_blank">jiao@tacc.utexas.edu</a>>, "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] problem running maker<br></div><div><br></div><div><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>Are you trying to install 2.26 or 2.10?</div>
<div><br></div><div>--Carson</div><div><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span>"Dian \"Oscar\" Jiao" <<a href="mailto:jiao@tacc.utexas.edu" target="_blank">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" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>[maker-devel] problem running maker<br></div><div><br></div><div dir="ltr"><div><div style="direction:ltr;font-size:10pt;font-family:Tahoma"><div style="font-family:Calibri,sans-serif;font-size:14px">
Hi, </div><div style="font-family:Calibri,sans-serif;font-size:14px"><br></div><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></div><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><div style="font-family:Calibri,sans-serif;font-size:14px"><br></div><div style="font-family:Calibri,sans-serif;font-size:14px">Oscar</div><div><br></div></div></div></div>
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