[adegenet-forum] new release 1.4-2

Tue May 13 07:48:29 CEST 2014

Dear all, 

we have just released a new version of adegenet (1.4-2) on CRAN. Binaries for windows and mac should be available within 48 hours. 

This version fixes known issues with the adegenetServer() function. The web tool we developed for DAPC should now be available to all. More on the website, as usual:
http://adegenet.r-forge.r-project.org/

Cheers
Thibaut

________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Jombart, Thibaut [t.jombart at imperial.ac.uk]
Sent: 12 May 2014 06:30
To: Xavier Giroux-Bougard
Cc: Caitlin Collins; adegenet-forum at lists.r-forge.r-project.org; Francesco Montinaro
Subject: Re: [adegenet-forum] adegenet-forum Digest, Vol 67, Issue 6

Hi there,

thanks for the positive feedback, and sorry about the late reply - I was trying to see where we're at with this problem. If I remember well, Caitlin identified the issue as a bug in shiny's latest version. I think she had a temporary fix for this (waiting for an update of shiny), but realize it's not been committed. We'll aim for a new release in the days to come to fix the issue.

Cheers
Thibaut

________________________________________
From: Xavier Giroux-Bougard [x.giroux.bougard at gmail.com]
Sent: 09 May 2014 01:22
To: Jombart, Thibaut
Cc: Caitlin Collins; Francesco Montinaro; adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] adegenet-forum Digest, Vol 67, Issue 6

Hello Caitlin and Jombart,

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:

Listening on http://127.0.0.1:5512
Error in substitute(value)[[2]] : subscript out of bounds
Error in if (!ONEDIM) { : argument is of length zero

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.

Am I doing anything wrong?

Thanks,

Xavier Giroux-Bougard

On Thu, Mar 20, 2014 at 11:48 AM, Jombart, Thibaut <t.jombart at imperial.ac.uk<mailto:t.jombart at imperial.ac.uk>> wrote:

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.

Cheers
Thibaut

________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org> [adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org>] on behalf of Caitlin Collins [caitiecollins at gmail.com<mailto:caitiecollins at gmail.com>]
Sent: 20 March 2014 13:52
To: Francesco Montinaro
Cc: adegenet-forum at lists.r-forge.r-project.org<mailto: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.

Best,
Caitlin.

On Thu, Mar 20, 2014 at 11:26 AM, Francesco Montinaro <francesco.montinaro at gmail.com<mailto:francesco.montinaro at gmail.com><mailto: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 http://127.0.0.1:7727
Error in substitute(value)[[2]] : subscript out of bounds
Error in if (!ONEDIM) { : argument is of length zero

Best,

Francesco

Francesco Montinaro

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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><mailto:t.jombart at imperial.ac.uk<mailto:t.jombart at imperial.ac.uk>>>
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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!

Best

Thibaut

--
######################################
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><mailto:t.jombart at imperial.ac.uk<mailto:t.jombart at imperial.ac.uk>>
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/

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