<div dir="ltr"><div><div><div><div><div>Hello Caitlin and Jombart,<br><br></div>big shout out to your work on the last release, your integration of a shiny app is particularly ingenious and forward thinking. Exploiting the richness of the Hadley ecosystem wherever we can promises access to innovative projects down the road. While I do not require it for my work, I wanted to try the adegenetServer() function for "show and tell" purposes and I get the same error as Francesco but on a windows machine:<br>
<br><span class="" style="border-collapse:separate;color:rgb(222,222,222);font-family:'Lucida Console';font-size:14px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:13px;text-indent:0px;text-transform:none;white-space:pre-wrap;word-spacing:0px;background-color:rgb(0,0,0)"></span><span class="" style="border-collapse:separate;color:rgb(222,222,222);font-family:'Lucida Console';font-size:14px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:13px;text-indent:0px;text-transform:none;white-space:pre-wrap;word-spacing:0px;background-color:rgb(0,0,0)"><pre tabindex="0" class="" style="font-family:'Lucida Console';font-size:10pt!important;outline-style:none;outline-width:initial;outline-color:initial;border-style:none;border-width:initial;border-color:initial;white-space:pre-wrap!important;word-break:break-all;margin:0px;line-height:1.2">
<span class="" style="color:rgb(231,140,69)">Listening on <a href="http://127.0.0.1:5512">http://127.0.0.1:5512</a>
</span><span class="" style="color:rgb(231,140,69)">Error in substitute(value)[[2]] : subscript out of bounds
</span><span class="" style="color:rgb(231,140,69)">Error in if (!ONEDIM) { : argument is of length zero</span></pre></span><br></div>While I chose to ignore these messages and focus on the browser (as per your instructions), the app is behaving a little erratically. It starts of bright, and then the app dims completely. While I can access all the tabs and the different options, there is no visual output. It seems as though the data is not loading at all.<br>
<br></div>Am I doing anything wrong?<br><br></div>Thanks,<br><br></div>Xavier Giroux-Bougard<br><div><br><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Mar 20, 2014 at 11:48 AM, Jombart, Thibaut <span dir="ltr"><<a href="mailto:t.jombart@imperial.ac.uk" target="_blank">t.jombart@imperial.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
Hi there,<br>
<br>
the web interface displays some messages, in particular warnings and errors, to the R console, but this does not mean that the interface itself is not working. As Caitlin said, depending on the state of the dialogue between the UI and the server, there may be transient errors but which actually don't stop the app from working.<br>
<br>
Is the web interface working at all on your computer? You may need to go back to your browser manually to see it.<br>
<br>
Cheers<br>
Thibaut<br>
<br>
<br>
________________________________________<br>
From: <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a> [<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>] on behalf of Caitlin Collins [<a href="mailto:caitiecollins@gmail.com">caitiecollins@gmail.com</a>]<br>
Sent: 20 March 2014 13:52<br>
To: Francesco Montinaro<br>
Cc: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
Subject: Re: [adegenet-forum] adegenet-forum Digest, Vol 67, Issue 6<br>
<div class=""><br>
Hi Francesco,<br>
<br>
Glad to see you are already testing out the new version of adegenet!<br>
<br>
I recognise the second message (Error in if (!ONEDIM) { : argument is of length zero). It appears twice in my R console upon start-up of the adegenetServer on Rstudio. It is also matched very briefly by the appearance of the truncated message (Error: argument is of length zero) in the adegenetServer browser. This occurs because the adegenetServer, upon start-up, attempts to immediately and simultaneously load the data and plot the DAPC scatterplot. This causes the plot function to return an error message in the moment before it is able to find the data. I will attempt to silence this error message in the next version of the adegenetServer. For now, unless you think the adegenetServer is otherwise misbehaving, I would say it is safe to simply ignore this error message.<br>
<br>
As for the first error message you mentioned (Error in substitute(value)[[2]] : subscript out of bounds), could you tell me when and where this is occurring, and also what processes it seems to be interrupting?<br>
<br>
Thank you for the feedback.<br>
<br>
Best,<br>
Caitlin.<br>
<br>
<br>
</div><div class="">On Thu, Mar 20, 2014 at 11:26 AM, Francesco Montinaro <<a href="mailto:francesco.montinaro@gmail.com">francesco.montinaro@gmail.com</a><mailto:<a href="mailto:francesco.montinaro@gmail.com">francesco.montinaro@gmail.com</a>>> wrote:<br>
Hi Thibaut,<br>
Thank you very much for this big update!<br>
<br>
When I type adegenetServer() on Rstudio (on Linuxmint)<br>
I get this error.<br>
<br>
Listening on <a href="http://127.0.0.1:7727" target="_blank">http://127.0.0.1:7727</a><br>
Error in substitute(value)[[2]] : subscript out of bounds<br>
Error in if (!ONEDIM) { : argument is of length zero<br>
<br>
<br>
Best,<br>
<br>
Francesco<br>
<br>
Francesco Montinaro<br>
<br>
<br>
</div><div class="">On 20 March 2014 11:00, <<a href="mailto:adegenet-forum-request@lists.r-forge.r-project.org">adegenet-forum-request@lists.r-forge.r-project.org</a><mailto:<a href="mailto:adegenet-forum-request@lists.r-forge.r-project.org">adegenet-forum-request@lists.r-forge.r-project.org</a>>> wrote:<br>
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Message: 1<br>
Date: Wed, 19 Mar 2014 17:02:12 +0000<br>
</div>From: "Jombart, Thibaut" <<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a><mailto:<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>>><br>
To: "<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><mailto:<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>>"<br>
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<div class="">Subject: [adegenet-forum] new release(s) of adegenet<br>
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</div> <<a href="mailto:2CB2DA8E426F3541AB1907F98ABA657075F77B9B@icexch-m1.ic.ac.uk">2CB2DA8E426F3541AB1907F98ABA657075F77B9B@icexch-m1.ic.ac.uk</a><mailto:<a href="mailto:2CB2DA8E426F3541AB1907F98ABA657075F77B9B@icexch-m1.ic.ac.uk">2CB2DA8E426F3541AB1907F98ABA657075F77B9B@icexch-m1.ic.ac.uk</a>>><br>
<div class="">Content-Type: text/plain; charset="Windows-1252"<br>
<br>
<br>
Dear all<br>
<br>
as some of you might have noticed, we have just released a new version of adegenet. Well, actually two, but 1.4-0 had a bug we had to correct quickly, so new version is 1.4-1.<br>
<br>
Big changes for this new release. The tutorials are no longer distributed as vignettes, but are accessible online from the adegenet website, or using the new command "adegenetTutorial". We have revamped the tutorials, which are now using knitr rather than Sweave (meaning: prettier, and easier to copy/paste command from the pdf into R).<br>
<br>
The other big news is that Caitlin and I have been working on a web server for DAPC, which is now part of the package. Type "adegenetServer()", and this will open up a web interface for DAPC. This includes some of the most recent work Caitlin has done on DAPC, like the feature selection procedure or the cross validation.<br>
<br>
As always, feedback and contributions welcome.<br>
<br>
Happy data analysis!<br>
<br>
Best<br>
<br>
Thibaut<br>
<br>
--<br>
######################################<br>
Dr Thibaut JOMBART<br>
MRC Centre for Outbreak Analysis and Modelling<br>
Department of Infectious Disease Epidemiology<br>
Imperial College - School of Public Health<br>
St Mary?s Campus<br>
Norfolk Place<br>
London W2 1PG<br>
United Kingdom<br>
Tel. : 0044 (0)20 7594 3658<br>
</div><a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a><mailto:<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>><br>
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