[adegenet-forum] adegenet-forum Digest, Vol 67, Issue 6

Jombart, Thibaut t.jombart at imperial.ac.uk
Thu Mar 20 16:48:58 CET 2014

Hi there, 

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. 

Is the web interface working at all on your computer? You may need to go back to your browser manually to see it.


From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Caitlin Collins [caitiecollins at gmail.com]
Sent: 20 March 2014 13:52
To: Francesco Montinaro
Cc: adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] adegenet-forum Digest, Vol 67, Issue 6

Hi Francesco,

Glad to see you are already testing out the new version of adegenet!

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.

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?

Thank you for the feedback.


On Thu, Mar 20, 2014 at 11:26 AM, Francesco Montinaro <francesco.montinaro at gmail.com<mailto:francesco.montinaro at gmail.com>> wrote:
Hi Thibaut,
Thank you very much for this big update!

When I type adegenetServer() on Rstudio (on Linuxmint)
I get this error.

Listening on
Error in substitute(value)[[2]] : subscript out of bounds
Error in if (!ONEDIM) { : argument is of length zero



Francesco Montinaro

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Today's Topics:

   1. new release(s) of adegenet (Jombart, Thibaut)


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Date: Wed, 19 Mar 2014 17:02:12 +0000
From: "Jombart, Thibaut" <t.jombart at imperial.ac.uk<mailto:t.jombart at imperial.ac.uk>>
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        <adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>>
Subject: [adegenet-forum] new release(s) of adegenet
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Dear all

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.

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).

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.

As always, feedback and contributions welcome.

Happy data analysis!



Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - School of Public Health
St Mary?s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk<mailto:t.jombart at imperial.ac.uk>


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