<div dir="ltr">Hi there, <div><br></div><div>I tried offline - can't reproduce the issue, it works fine for me with:</div><div><br></div><div><div><font face="monospace, monospace">> R.version</font></div><div><font face="monospace, monospace"> _ </font></div><div><font face="monospace, monospace">platform x86_64-pc-linux-gnu </font></div><div><font face="monospace, monospace">arch x86_64 </font></div><div><font face="monospace, monospace">os linux-gnu </font></div><div><font face="monospace, monospace">system x86_64, linux-gnu </font></div><div><font face="monospace, monospace">status </font></div><div><font face="monospace, monospace">major 3 </font></div><div><font face="monospace, monospace">minor 3.1 </font></div><div><font face="monospace, monospace">year 2016 </font></div><div><font face="monospace, monospace">month 06 </font></div><div><font face="monospace, monospace">day 21 </font></div><div><font face="monospace, monospace">svn rev 70800 </font></div><div><font face="monospace, monospace">language R </font></div><div><font face="monospace, monospace">version.string R version 3.3.1 (2016-06-21)</font></div><div><font face="monospace, monospace">nickname Bug in Your Hair </font></div></div><div><div><font face="monospace, monospace">> sessionInfo()</font></div><div><font face="monospace, monospace">R version 3.3.1 (2016-06-21)</font></div><div><font face="monospace, monospace">Platform: x86_64-pc-linux-gnu (64-bit)</font></div><div><font face="monospace, monospace">Running under: Ubuntu 14.04.4 LTS</font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">locale:</font></div><div><font face="monospace, monospace"> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C </font></div><div><font face="monospace, monospace"> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 </font></div><div><font face="monospace, monospace"> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 </font></div><div><font face="monospace, monospace"> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C </font></div><div><font face="monospace, monospace"> [9] LC_ADDRESS=C LC_TELEPHONE=C </font></div><div><font face="monospace, monospace">[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C </font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">attached base packages:</font></div><div><font face="monospace, monospace">[1] stats graphics grDevices utils datasets methods base </font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">other attached packages:</font></div><div><font face="monospace, monospace">[1] adegenet_2.0.1 ade4_1.7-4 covr_2.2.0 testthat_1.0.2 </font></div><div><font face="monospace, monospace">[5] knitr_1.13 devtools_1.12.0</font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">loaded via a namespace (and not attached):</font></div><div><font face="monospace, monospace"> [1] Rcpp_0.12.6 spdep_0.6-6 plyr_1.8.4 LearnBayes_2.15 </font></div><div><font face="monospace, monospace"> [5] tools_3.3.1 boot_1.3-18 digest_0.6.10 memoise_1.0.0 </font></div><div><font face="monospace, monospace"> [9] tibble_1.1 gtable_0.2.0 nlme_3.1-128 lattice_0.20-33 </font></div><div><font face="monospace, monospace">[13] mgcv_1.8-13 Matrix_1.2-6 rex_1.1.1 igraph_1.0.1 </font></div><div><font face="monospace, monospace">[17] shiny_0.13.2.9004 DBI_0.4-1 parallel_3.3.1 coda_0.18-1 </font></div><div><font face="monospace, monospace">[21] cluster_2.0.4 withr_1.0.2 dplyr_0.5.0 stringr_1.0.0 </font></div><div><font face="monospace, monospace">[25] gtools_3.5.0 grid_3.3.1 R6_2.1.2 sp_1.2-3 </font></div><div><font face="monospace, monospace">[29] gdata_2.17.0 ggplot2_2.1.0 reshape2_1.4.1 seqinr_3.3-0 </font></div><div><font face="monospace, monospace">[33] deldir_0.1-12 magrittr_1.5 gmodels_2.16.2 splines_3.3.1 </font></div><div><font face="monospace, monospace">[37] scales_0.4.0 htmltools_0.3.5 MASS_7.3-45 assertthat_0.1 </font></div><div><font face="monospace, monospace">[41] permute_0.9-0 mime_0.5 ape_3.5 colorspace_1.2-6 </font></div><div><font face="monospace, monospace">[45] xtable_1.8-2 httpuv_1.3.3 stringi_1.1.1 lazyeval_0.2.0 </font></div><div><font face="monospace, monospace">[49] munsell_0.4.3 vegan_2.4-0 crayon_1.3.2 </font></div></div><div><br></div><div><br></div><div>If the problem persists on the current version of R and adegenet, please post an issue and we'll try to reproduce the problem.</div><div><br></div><div>Best</div><div>Thibaut</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div><div><br>--<br>Dr Thibaut Jombart<br>Lecturer, Department of Infectious Disease Epidemiology<br></div></div>Imperial College London<br><a href="https://sites.google.com/site/thibautjombart/" target="_blank">https://sites.google.com/site/thibautjombart/</a><br></div><div><a href="https://github.com/thibautjombart" target="_blank">https://github.com/thibautjombart<br></a></div>Twitter: <a href="https://twitter.com/TeebzR" target="_blank">@TeebzR</a><br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On 5 August 2016 at 11:35, Mark Coulson <span dir="ltr"><<a href="mailto:Mark.Coulson.ic@uhi.ac.uk" target="_blank">Mark.Coulson.ic@uhi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Ok,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">So got it working now by omitting the D <- as.matrix(X) step and running the hclust only from the D <- dist(X)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">M<u></u><u></u></span></p><span class="">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<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"> Thibaut Jombart [mailto:<a href="mailto:thibautjombart@gmail.com" target="_blank">thibautjombart@gmail.<wbr>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.<wbr>r-project.org</a><br>
<b>Subject:</b> Re: [adegenet-forum] error in hclust<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Odd indeed. Are there any NAs in 'X'?<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Cheers<u></u><u></u></p>
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<p class="MsoNormal">Thibaut<u></u><u></u></p>
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--<br>
Dr Thibaut Jombart<br>
Lecturer, Department of Infectious Disease Epidemiology<u></u><u></u></p>
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<p class="MsoNormal">Imperial College London<br>
<a href="https://sites.google.com/site/thibautjombart/" target="_blank">https://sites.google.com/site/<wbr>thibautjombart/</a><u></u><u></u></p>
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<p class="MsoNormal"><a href="https://github.com/thibautjombart" target="_blank">https://github.com/<wbr>thibautjombart<br>
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<p class="MsoNormal">Twitter: <a href="https://twitter.com/TeebzR" target="_blank">
@TeebzR</a><u></u><u></u></p>
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<p class="MsoNormal">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:<u></u><u></u></p>
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<p class="MsoNormal">Hello,<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">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<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">laidon <- import2genind("laidon_project_<wbr>data_no_sibs.str")<u></u><u></u></p>
<p class="MsoNormal">X <- tab(laidon, freq=TRUE, NA.method="mean")
<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">D <- dist(X)<u></u><u></u></p>
<p class="MsoNormal">D <- as.matrix(D)<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">h1 <- hclust(D, method="complete")<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></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") :
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<p class="MsoNormal" style="line-height:11.25pt;background:white;word-break:break-all">
<span style="font-size:10.0pt;font-family:"Lucida Console";color:#c5060b"> missing value where TRUE/FALSE needed</span><u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Not sure what this error means but more confused as to why suddenly it isn’t working. Nothing else has changed<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Mark<u></u><u></u></p>
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<p class="MsoNormal">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.
<u></u><u></u></p>
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______________________________<wbr>_________________<br>
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<p class="MsoNormal"><u></u> <u></u></p>
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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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