<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div><span class="Apple-style-span" style="font-family: Calibri; font-size: medium; "> </span><span class="Apple-style-span" style="font-family: Calibri; font-size: medium; ">//=</span><span class="Apple-style-span" style="font-family: Calibri; font-size: medium; "> is a feature of perl versions 5.10 and above.</span></div><div><span class="Apple-style-span" style="font-family: Calibri; font-size: medium; "><br></span></div><div><span class="Apple-style-span" style="font-family: Calibri; font-size: medium; ">You must have an older version of perl.</span></div><div><span class="Apple-style-span" style="font-family: Calibri; font-size: medium; ">Just change it to ||= and it will work for older versions. I'll make that change to the release as well to make it work with older perl.</span></div><div><span class="Apple-style-span" style="font-family: Calibri; font-size: medium; "><br></span></div><div><span class="Apple-style-span" style="font-family: Calibri; font-size: medium; ">Thanks,</span></div><div><span class="Apple-style-span" style="font-family: Calibri; font-size: medium; ">Carson</span></div><div><span class="Apple-style-span" style="font-family: Calibri; font-size: medium; "><br></span></div><div><span class="Apple-style-span" style="font-family: Calibri; font-size: medium; "><br></span></div><div><span class="Apple-style-span" style="font-family: Calibri; font-size: medium; "><br></span></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Evan Ernst <<a href="mailto:eernst@cshl.edu">eernst@cshl.edu</a>><br><span style="font-weight:bold">Date: </span> Mon, 26 Mar 2012 16:13:19 -0400<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> <<a href="mailto:maker-devel@googlegroups.com">maker-devel@googlegroups.com</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Can't call method "start" on an undefined value<br></div><div><br></div>Hi Carson,<div><br></div><div>Line 242 of maker is causing a compilation failure in the version I downloaded:</div><div><br></div><div><div>241 -> eval "\$ver = \$${name}::VERSION";</div><div>242 -> $ver //= 'UNKNOWN';</div><div>243 -> $ver = 'UNKNOWN' if($ver =~ /^\-1\,/);</div></div><div><br></div><div>Thanks,</div><div>Evan<br><br><div class="gmail_quote">On Mon, Mar 26, 2012 at 3:06 PM, Evan Ernst <span dir="ltr"><<a href="mailto:eernst@cshl.edu" target="_blank">eernst@cshl.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Fantastic. Thanks for your help.<div><br></div><div>Best,</div><div>Evan<div><div><br><br><div class="gmail_quote">
On Mon, Mar 26, 2012 at 3:05 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><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>Ok. This is fixed (along with a few other things), and is available for download as MAKER 2.25.</div><div><div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></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> Evan <<a href="mailto:eernst@cshl.edu" target="_blank">eernst@cshl.edu</a>><br><span style="font-weight:bold">Date: </span> Mon, 26 Mar 2012 09:29:45 -0700 (PDT)<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@googlegroups.com" target="_blank">maker-devel@googlegroups.com</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Can't call method "start" on an undefined value<br></div><div><br></div>Hi,<br><br>I'm running maker 2.24-beta. At least 10-15% of scaffolds are failing with the following error:<br><span style="font-family: 'courier new', monospace; "></span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; ">Preparing evidence for hint based annotation</span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; ">cleaning clusters....</span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; ">total clusters:1 now processing 0</span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; ">in cluster::shadow_cluster...</span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; ">...finished clustering.</span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; ">cleaning clusters....</span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; ">total clusters:4 now processing 0</span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; "> ...processing 0 of 3</span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; "> ...processing 1 of 3</span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; ">total clusters:4 now processing 0</span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; "> ...processing 0 of 2</span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; ">total clusters:4 now processing 0</span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; ">total clusters:4 now processing 0</span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; ">Can't call method "start" on an undefined valueERROR: Failed while preparing evidence clusters for annotations</span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; ">ERROR: Chunk failed at level:0, tier_type:3</span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; ">FAILED CONTIG:scaffold93.1</span><br style="font-family:courier new,monospace"><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; ">ERROR: Chunk failed at level:7, tier_type:0</span><br style="font-family:courier new,monospace"><span style="font-family: 'courier new', monospace; ">FAILED CONTIG:scaffold93.1</span><br style="font-family:courier new,monospace"><br>This occurs when running just a single maker instance. <br><br>Thanks,<br>Evan<br>_______________________________________________
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<a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></span></div></div></div></blockquote></div><br><br clear="all"><div><br></div></div></div><div>-- <br>Evan Ernst<div>Martienssen Lab</div><div><br></div><div>Delbruck #216</div><div>Cold Spring Harbor Laboratory</div><div>1 Bungtown Rd.</div><div>Cold Spring Harbor, NY 11724</div><br></div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Evan Ernst<div>Martienssen Lab</div><div><br></div><div>Delbruck #216</div><div>Cold Spring Harbor Laboratory</div><div>1 Bungtown Rd.</div><div>Cold Spring Harbor, NY 11724</div><br></div></span></body></html>