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

Fri May 9 02:22:22 CEST 2014

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://127.0.0.1:5512Error in substitute(value)[[2]] :
subscript out of boundsError 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
> 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 [
> 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.
>
> Best,
> Caitlin.
>
>
> 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 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
>
>
> On 20 March 2014 11:00, <
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>    1. new release(s) of adegenet (Jombart, Thibaut)
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> ----------------------------------------------------------------------
>
> Message: 1
> 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>>
> To: "adegenet-forum at lists.r-forge.r-project.org<mailto:
> adegenet-forum at lists.r-forge.r-project.org>"
>         <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
> Message-ID:
>         <2CB2DA8E426F3541AB1907F98ABA657075F77B9B at icexch-m1.ic.ac.uk
> <mailto:2CB2DA8E426F3541AB1907F98ABA657075F77B9B at icexch-m1.ic.ac.uk>>
> Content-Type: text/plain; charset="Windows-1252"
>
>
> 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>
> http://sites.google.com/site/thibautjombart/
> http://adegenet.r-forge.r-project.org/
>
> ------------------------------
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