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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">I ran exactly that same script.
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Roman Luštrik [mailto:roman.lustrik@biolitika.si]
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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<o:p></o:p></span></p>
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<p class="MsoNormal"><span 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?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Trebuchet MS",sans-serif;color:black">Cheers,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Trebuchet MS",sans-serif;color:black">Roman<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Trebuchet MS",sans-serif;color:black">----<br>
In god we trust, all others bring data.<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:"Trebuchet MS",sans-serif;color:black">From:
</span></b><span style="font-family:"Trebuchet MS",sans-serif;color:black">"Mark Coulson" <<a href="mailto:Mark.Coulson.ic@uhi.ac.uk">Mark.Coulson.ic@uhi.ac.uk</a>><br>
<b>To: </b>"Thibaut Jombart" <<a href="mailto:thibautjombart@gmail.com">thibautjombart@gmail.com</a>><br>
<b>Cc: </b><a href="mailto:adegenet-forum@lists.r-forge.r-project.org">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<o:p></o:p></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">There are but this should be taken care of by NA.method and again worked just fine yesterday!</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Mark</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" 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"> Thibaut Jombart [<a href="mailto:thibautjombart@gmail.com">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">Mark.Coulson.ic@uhi.ac.uk</a>><br>
<b>Cc:</b> <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
<b>Subject:</b> Re: [adegenet-forum] error in hclust</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Odd indeed. Are there any NAs in 'X'?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Cheers<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Thibaut<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"><br>
--<br>
Dr Thibaut Jombart<br>
Lecturer, Department of Infectious Disease Epidemiology<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Imperial College London<br>
<a href="https://sites.google.com/site/thibautjombart/" target="_blank">https://sites.google.com/site/thibautjombart/</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"><a href="https://github.com/thibautjombart" target="_blank">https://github.com/thibautjombart<br>
</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Twitter: <a href="https://twitter.com/TeebzR" target="_blank">
@TeebzR</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span 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:<o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Hello,<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span 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<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">laidon <- import2genind("laidon_project_data_no_sibs.str")<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">X <- tab(laidon, freq=TRUE, NA.method="mean")
<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">D <- dist(X)<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">D <- as.matrix(D)<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">h1 <- hclust(D, method="complete")<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> <o:p></o:p></span></p>
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<span 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") :
</span><span style="color:black"><o:p></o:p></span></p>
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<span style="font-size:10.0pt;font-family:"Lucida Console";color:#C5060B"> missing value where TRUE/FALSE needed</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Not sure what this error means but more confused as to why suddenly it isn’t working. Nothing else has changed<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Mark<o:p></o:p></span></p>
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<p class="MsoNormal"><span 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.
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span 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">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.
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