<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Continuous chars still seem to be loaded okay, but standard fails as Conrad indicates.<div><br></div><div>I'm not sure if this is related to the changes in readNCL/NCL interface code/NCL that might be causing this issue, but phylobase now crashes R if given a poorly-formatted nexus file or given an incorrect path to a nexus file (at least on a Mac OS 10.6.4 with R2.11.1).</div><div><br></div><div>Brian</div><div><br></div><div><div><div>On Aug 3, 2010, at 5:42 PM, Conrad Stack wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">I just upgraded to phylobase 0.6.1 and found that the data in my CHARACTERS blocks are no longer being read in (they show up as blanks in the returned phylo4d object).<div><br></div><div>this is from the geospiza.nex dataset:</div>
<div><div><br></div><div>BEGIN CHARACTERS;</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>DIMENSIONS NCHAR=1;</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>MATRIX</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>fuliginosa 1</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>fortis 1</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>magnirostris 0</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>conirostris 0</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>scandens 0</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>difficilis 1</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>pallida 0</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>parvulus 0</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>psittacula 0</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>pauper 0</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Platyspiza 0</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>fusca 0</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Pinaroloxias 0</div><div><br></div><div>;</div><div><br></div><div>
END;</div><div><br></div><div>When it reads in, it shows up like this:</div><div><div>readNexus("geospiza.nex")</div><div> label node ancestor edge.length node.type standard_char</div><div>1 fuliginosa 1 22 0.05500 tip </div>
<div>2 fortis 2 22 0.05500 tip </div><div>3 magnirostris 3 21 0.11000 tip </div><div>4 conirostris 4 20 0.18333 tip </div>
<div>5 scandens 5 19 0.19250 tip </div><div>6 difficilis 6 18 0.22800 tip </div><div>7 pallida 7 23 0.08667 tip </div>
<div>8 parvulus 8 25 0.02000 tip </div><div>9 psittacula 9 25 0.02000 tip </div><div>10 pauper 10 24 0.03500 tip </div>
<div>11 Platyspiza 11 16 0.46550 tip </div><div>12 fusca 12 15 0.53409 tip </div><div>13 Pinaroloxias 13 14 0.58333 tip </div>
<div>14 <NA> 14 0 0.29744 root <NA></div><div>15 <NA> 15 14 0.04924 internal <NA></div><div>16 <NA> 16 15 0.06859 internal <NA></div>
</div>.......cont....</div><div><br></div><div>Any thoughts? (I'm using windows 7 32-bit with R 2.11, but the error occurs on my Mac leopard install as well.</div><div><br></div><div><br clear="all"><br>-- <br>Conrad Stack<br>
-----------------------<br>PSU Department of Biology<br>208 Mueller Lab <br>University Park, PA 16802<br>cell: 814.409.8310<br>email: <a href="mailto:conrad.stack@gmail.com">conrad.stack@gmail.com</a><br>
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