Bugs while running

[smhoban]

Thanks for squashing the bug I mentioned last week with "analysis_funcs". No problems there now.

New error. When I go to "General Conf" and click "Coalescent simulator?" checkbox I get:

Warning: Error in observeEventHandler: no slot of name "inf.site.model" for this object of class "fastsimcoal.params" Stack trace (innermost first): 64: observeEventHandler [make-skelesim-class.R#262] 2: runApp 1: skeleSimGUI [1] "numloci 1" Warning: Error in : assignment of an object of class “matrix” is not valid for @‘locus.params’ in an object of class “fastsimcoal.params”; is(value, "dfOrNULL") is not TRUE Stack trace (innermost first): 65: 64: observeEventHandler [simcoal-server.R#131] 2: runApp 1: skeleSimGUI Warning: Error in observeEventHandler: no slot of name "inf.site.model" for this object of class "fastsimcoal.params" Stack trace (innermost first): 64: observeEventHandler [make-skelesim-class.R#262] 2: runApp 1: skeleSimGUI

[EricArcher]

This is due to the new fastsimcoal input format. It is now a data.frame where before it was a matrix. The columns are also somewhat different.

Also, the slot, "inf.site.model" has been removed.

[smhoban]

Thanks. All: I'm finding various ways to break skelesim or various questions or quirks as I go through the user guide. These are going in one issue (#26) for now. Nothing urgent but some things to work on.

On Mon, Mar 7, 2016 at 9:52 AM, Eric Archer notifications@github.com wrote:

This is due to the new fastsimcoal input format. It is now a data.frame where before it was a matrix. The columns are also somewhat different.

— Reply to this email directly or view it on GitHub https://github.com/christianparobek/skeleSim/issues/25#issuecomment-193311330 .

Sean Hoban Tree Conservation Biologist The Morton Arboretum http://www.mortonarb.org/ 4100 Illinois Rt 53, 3rd Floor Research Bldg, room 324, Lisle, IL 630-719-2419

New publications!! Accounting for the nested nature of genetic variation http://onlinelibrary.wiley.com/doi/10.1111/oik.02760/abstract Oikos 2016 Exploring seaweed population dynamics http://onlinelibrary.wiley.com/doi/10.1111/jpy.12366/abstract Journal of Phycology 2016 Loci under selection in expanding tree populations http://onlinelibrary.wiley.com/doi/10.1111/mec.13234/abstract Molecular Ecology 2015 Designing optimal seed collection protocols http://www.sciencedirect.com/science/article/pii/S0006320715001767 Biological Conservation 2015 Using ABC to understand invasive species establishment http://www.nature.com/hdy/journal/vaop/ncurrent/full/hdy201538a.html Heredity 2015

research webpage: http://sites.google.com/site/hoban3/ ResearchGate Profile: http://www.researchgate.net/profile/Sean_Hoban/ food blog: http://cuisineraveclevin.blogspot.it/ blog about invasive species: http://invasivore.org/

[smhoban]

Lastly, I might be missing out on something but now that I've got my test skelesim object prepared, with two scenarios, I click "Run simulation" and nothing happens. Well, I get "Wrote skeleSim parameter file: '/home/user/Documents/test.20160308.1230.6079.params.rdata'" but this just has my skelesim object but no results.

Can someone try to load this object and run it, and tell me what I'm missing :) I'll put this object in the main directory: test.20160308.1226.2546.params.rdata

[smhoban]

Now I've pulled everything and I get the following error which I didn't get before:

Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class. Warning: Error in is.data.frame: object 'result' not found Stack trace (innermost first): 49: is.data.frame 48: colnames 47: match 46: %in% 45: eval [visualize.R#26] 44: eval 43: withVisible 42: source 41: server [/home/user/R/x86_64-pc-linux-gnu-library/3.2/skeleSim/shiny/skeleSimShinyGUI/server.R#53] 2: runApp 1: skeleSimGUI Error in is.data.frame(x) : object 'result' not found

[MichelleDBG]

How about this error (after "Coalescent simulator" is selected)

Warning: Error in observeEventHandler: no slot of name "inf.site.model" for this object of class "fastsimcoal.params" Stack trace (innermost first): 64: observeEventHandler [make-skelesim-class.R#262] 2: runApp 1: skeleSimGUI [1] "numloci 1" Warning: Error in : assignment of an object of class “matrix” is not valid for @‘locus.params’ in an object of class “fastsimcoal.params”; is(value, "dfOrNULL") is not TRUE Stack trace (innermost first): 65: 64: observeEventHandler [simcoal-server.R#131] 2: runApp 1: skeleSimGUI Warning: Error in observeEventHandler: no slot of name "inf.site.model" for this object of class "fastsimcoal.params" Stack trace (innermost first): 64: observeEventHandler [make-skelesim-class.R#262] 2: runApp 1: skeleSimGUI [1] "numloci 1" Warning: Error in : assignment of an object of class “matrix” is not valid for @‘locus.params’ in an object of class “fastsimcoal.params”; is(value, "dfOrNULL") is not TRUE Stack trace (innermost first): 65: 64: observeEventHandler [simcoal-server.R#131] 2: runApp 1: skeleSimGUI ERROR: [on_request_read] connection reset by peer

[smhoban]

Me too! I think Allan was chasing this one..

On Thu, Mar 10, 2016 at 2:45 PM, Michelle DePrenger-Levin < notifications@github.com> wrote:

How about this error (after "Coalescent simulator" is selected)

Warning: Error in observeEventHandler: no slot of name "inf.site.model" for this object of class "fastsimcoal.params" Stack trace (innermost first): 64: observeEventHandler [make-skelesim-class.R#262] 2: runApp 1: skeleSimGUI [1] "numloci 1" Warning: Error in : assignment of an object of class “matrix” is not valid for @‘locus.params’ in an object of class “fastsimcoal.params”; is(value, "dfOrNULL") is not TRUE Stack trace (innermost first): 65: 64: observeEventHandler [simcoal-server.R#131] 2: runApp 1: skeleSimGUI Warning: Error in observeEventHandler: no slot of name "inf.site.model" for this object of class "fastsimcoal.params" Stack trace (innermost first): 64: observeEventHandler [make-skelesim-class.R#262] 2: runApp 1: skeleSimGUI [1] "numloci 1" Warning: Error in : assignment of an object of class “matrix” is not valid for @‘locus.params’ in an object of class “fastsimcoal.params”; is(value, "dfOrNULL") is not TRUE Stack trace (innermost first): 65: 64: observeEventHandler [simcoal-server.R#131] 2: runApp 1: skeleSimGUI ERROR: [on_request_read] connection reset by peer

— Reply to this email directly or view it on GitHub https://github.com/christianparobek/skeleSim/issues/25#issuecomment-195038840 .

Sean Hoban Tree Conservation Biologist The Morton Arboretum http://www.mortonarb.org/ 4100 Illinois Rt 53, 3rd Floor Research Bldg, room 324, Lisle, IL 630-719-2419

New publications!! Accounting for the nested nature of genetic variation http://onlinelibrary.wiley.com/doi/10.1111/oik.02760/abstract Oikos 2016 Exploring seaweed population dynamics http://onlinelibrary.wiley.com/doi/10.1111/jpy.12366/abstract Journal of Phycology 2016 Loci under selection in expanding tree populations http://onlinelibrary.wiley.com/doi/10.1111/mec.13234/abstract Molecular Ecology 2015 Designing optimal seed collection protocols http://www.sciencedirect.com/science/article/pii/S0006320715001767 Biological Conservation 2015 Using ABC to understand invasive species establishment http://www.nature.com/hdy/journal/vaop/ncurrent/full/hdy201538a.html Heredity 2015

research webpage: http://sites.google.com/site/hoban3/ ResearchGate Profile: http://www.researchgate.net/profile/Sean_Hoban/ food blog: http://cuisineraveclevin.blogspot.it/ blog about invasive species: http://invasivore.org/

[smhoban]

I'm still getting the same error that Michelle and I got (above) when we click on 'coalescent simulation'. This is a pretty big one because you can't get past it and so can't do any coalescent simulations- the whole system crashes. Anyone on this one?

[stranda]

Ok Now I see that Eric had already removed int.site.model on purpose. It is now removed from the ui. I still have growth rates and sample times re-added. Do I need to remove those inputs from the ui as well?

[smhoban]

Works for me now. Anyway I can click on coalescent without crashing it. So that is a start!

[EricArcher]

Sorry I'm getting to this late. You guys have nailed the cause. Allan, growth rates and sample times are input as part of the single fsc.loadScenario function now. Let me know if you've got other questions on that.

[stranda]

I think this one is closed