<html><body><div style="font-family: trebuchet ms,sans-serif; font-size: 12pt; color: #000000"><div>Hi,</div><div><br data-mce-bogus="1"></div><div>it would be great if you could whip up a small reproducible example (you could consider creating a gist at e.g. gist.github.com) which demonstrates this problem. Without the data and code in hand, it's really all just speculation.</div><div><br data-mce-bogus="1"></div><div>Cheers,</div><div>Roman</div><div><br></div><div data-marker="__SIG_PRE__">----<br>In god we trust, all others bring data.</div><br><hr id="zwchr" data-marker="__DIVIDER__"><div data-marker="__HEADERS__"><b>From: </b>"Mark Coulson" <Mark.Coulson.ic@uhi.ac.uk><br><b>To: </b>"Roman Luštrik" <roman.lustrik@biolitika.si><br><b>Cc: </b>"Thibaut Jombart" <thibautjombart@gmail.com>, adegenet-forum@lists.r-forge.r-project.org<br><b>Sent: </b>Friday, August 5, 2016 11:54:30 AM<br><b>Subject: </b>RE: [adegenet-forum] error in hclust<br></div><br><div data-marker="__QUOTED_TEXT__">
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<p class="MsoNormal"><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;" data-mce-style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;">I ran exactly that same script.
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<b>Sent:</b> 05 August 2016 10:52<br>
<b>To:</b> Mark Coulson <Mark.Coulson.ic@uhi.ac.uk><br>
<b>Cc:</b> Thibaut Jombart <thibautjombart@gmail.com>; adegenet-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> Re: [adegenet-forum] error in hclust</span></p>
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<p class="MsoNormal"><span style="font-family: 'Trebuchet MS',sans-serif; color: black;" data-mce-style="font-family: 'Trebuchet MS',sans-serif; color: black;">It's not entirely clear what you've done yesterday. Can you provide a reproducible example?</span></p>
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<p class="MsoNormal"><span style="font-family: 'Trebuchet MS',sans-serif; color: black;" data-mce-style="font-family: 'Trebuchet MS',sans-serif; color: black;">Cheers,</span></p>
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<p class="MsoNormal"><span style="font-family: 'Trebuchet MS',sans-serif; color: black;" data-mce-style="font-family: 'Trebuchet MS',sans-serif; color: black;">----<br>
In god we trust, all others bring data.</span></p>
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<p class="MsoNormal"><b><span style="font-family: 'Trebuchet MS',sans-serif; color: black;" data-mce-style="font-family: 'Trebuchet MS',sans-serif; color: black;">From:
</span></b><span style="font-family: 'Trebuchet MS',sans-serif; color: black;" data-mce-style="font-family: 'Trebuchet MS',sans-serif; color: black;">"Mark Coulson" <<a href="mailto:Mark.Coulson.ic@uhi.ac.uk" target="_blank">Mark.Coulson.ic@uhi.ac.uk</a>><br>
<b>To: </b>"Thibaut Jombart" <<a href="mailto:thibautjombart@gmail.com" target="_blank">thibautjombart@gmail.com</a>><br>
<b>Cc: </b><a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge.r-project.org</a><br>
<b>Sent: </b>Friday, August 5, 2016 11:42:48 AM<br>
<b>Subject: </b>Re: [adegenet-forum] error in hclust</span></p>
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<p class="MsoNormal"><span style="font-family: 'Trebuchet MS',sans-serif; color: black;" data-mce-style="font-family: 'Trebuchet MS',sans-serif; color: black;"> </span></p>
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<p class="MsoNormal"><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;" data-mce-style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;">There are but this should be taken care of by NA.method and again worked just fine yesterday!</span><span style="color: black;" data-mce-style="color: black;"></span></p>
<p class="MsoNormal"><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;" data-mce-style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;"> </span><span style="color: black;" data-mce-style="color: black;"></span></p>
<p class="MsoNormal"><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;" data-mce-style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;">Mark</span><span style="color: black;" data-mce-style="color: black;"></span></p>
<p class="MsoNormal"><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;" data-mce-style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;"> </span><span style="color: black;" data-mce-style="color: black;"></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: black;" data-mce-style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: black;">From:</span></b><span lang="EN-US" style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: black;" data-mce-style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: black;"> Thibaut Jombart [<a href="mailto:thibautjombart@gmail.com" target="_blank">mailto:thibautjombart@gmail.com</a>]
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<b>Sent:</b> 05 August 2016 10:41<br>
<b>To:</b> Mark Coulson <<a href="mailto:Mark.Coulson.ic@uhi.ac.uk" target="_blank">Mark.Coulson.ic@uhi.ac.uk</a>><br>
<b>Cc:</b> <a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge.r-project.org</a><br>
<b>Subject:</b> Re: [adegenet-forum] error in hclust</span><span style="color: black;" data-mce-style="color: black;"></span></p>
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<p class="MsoNormal"><span style="color: black;" data-mce-style="color: black;">Odd indeed. Are there any NAs in 'X'?</span></p>
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<p class="MsoNormal"><span style="color: black;" data-mce-style="color: black;">Cheers</span></p>
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<p class="MsoNormal"><span style="color: black;" data-mce-style="color: black;">Thibaut</span></p>
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--<br>
Dr Thibaut Jombart<br>
Lecturer, Department of Infectious Disease Epidemiology</span></p>
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<p class="MsoNormal"><span style="color: black;" data-mce-style="color: black;">Imperial College London<br>
<a href="https://sites.google.com/site/thibautjombart/" target="_blank">https://sites.google.com/site/thibautjombart/</a></span></p>
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<p class="MsoNormal"><span style="color: black;" data-mce-style="color: black;">Twitter: <a href="https://twitter.com/TeebzR" target="_blank">
@TeebzR</a></span></p>
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<p class="MsoNormal"><span style="color: black;" data-mce-style="color: black;">On 5 August 2016 at 10:34, Mark Coulson <<a href="mailto:Mark.Coulson.ic@uhi.ac.uk" target="_blank">Mark.Coulson.ic@uhi.ac.uk</a>> wrote:</span></p>
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<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;" data-mce-style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: black;" data-mce-style="color: black;">Hello,</span></p>
<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;" data-mce-style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: black;" data-mce-style="color: black;"> </span></p>
<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;" data-mce-style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: black;" data-mce-style="color: black;">Yesterday I ran the following code and everything worked just fine. Today I simply opened up my script and re-ran it and got the following</span></p>
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<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;" data-mce-style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: black;" data-mce-style="color: black;">laidon <- import2genind("laidon_project_data_no_sibs.str")</span></p>
<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;" data-mce-style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: black;" data-mce-style="color: black;">X <- tab(laidon, freq=TRUE, NA.method="mean")
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<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;" data-mce-style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: black;" data-mce-style="color: black;">D <- dist(X)</span></p>
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<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;" data-mce-style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: black;" data-mce-style="color: black;">h1 <- hclust(D, method="complete")</span></p>
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<span style="font-size: 10.0pt; font-family: 'Lucida Console'; color: #c5060b;" data-mce-style="font-size: 10.0pt; font-family: 'Lucida Console'; color: #c5060b;">Error in if (<a href="http://is.na" target="_blank">is.na</a>(n) || n > 65536L) stop("size cannot be NA nor exceed 65536") :
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<span style="font-size: 10.0pt; font-family: 'Lucida Console'; color: #c5060b;" data-mce-style="font-size: 10.0pt; font-family: 'Lucida Console'; color: #c5060b;"> missing value where TRUE/FALSE needed</span><span style="color: black;" data-mce-style="color: black;"></span></p>
<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;" data-mce-style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: black;" data-mce-style="color: black;"> </span></p>
<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;" data-mce-style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: black;" data-mce-style="color: black;">Not sure what this error means but more confused as to why suddenly it isn’t working. Nothing else has changed</span></p>
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<p class="MsoNormal"><span style="color: black;" data-mce-style="color: black;">Inverness College UHI, a partner in the University of the Highlands and Islands
<a href="http://www.inverness.uhi.ac.uk" target="_blank">www.inverness.uhi.ac.uk</a> Board of Management of Inverness College (known as Inverness College UHI), Scottish Charity No SC021197.
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_______________________________________________<br>
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<p class="MsoNormal"><span style="font-family: 'Trebuchet MS',sans-serif; color: black;" data-mce-style="font-family: 'Trebuchet MS',sans-serif; color: black;">Inverness College UHI, a partner in the University of the Highlands and Islands
<a href="http://www.inverness.uhi.ac.uk" target="_blank">www.inverness.uhi.ac.uk</a> Board of Management of Inverness College (known as Inverness College UHI), Scottish Charity No SC021197.
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Inverness College UHI, a partner in the University of the Highlands and Islands www.inverness.uhi.ac.uk Board of Management of Inverness College (known as Inverness College UHI), Scottish Charity No SC021197.<br></div></div></body></html>