first time running skeleSim GUI

[smhoban]

I followed the instructions here, and got through installing and loading skelesim (library) and that worked fine, but the command skeleSimGUI() results in: Error: could not find function "skeleSimGUI" Has it been renamed?

[stranda]

Hmm. Should be able to (after Install): library(skeleSim) skeleSimGUI()

Works on my linux machine, I'm installing on windows now to check

[smhoban]

Same error on Ubuntu...

install.packages("skeleSim_0.9.tar.gz") library(skeleSim) skeleSimGUI() Error: could not find function "skeleSimGUI"

[stranda]

may be a version problem on ubuntu, can you try: library(devtools) install_github("christianparobek/skeleSim/skeleSim",force=T)

[smhoban]

I also managed to get this error. Do I need the rmetasim from github?

Error : package 'rmetasim' 2.0.4 was found, but >= 3.0.0 is required by 'skeleSim' ERROR: lazy loading failed for package 'skeleSim'

On Sun, Feb 21, 2016 at 5:09 PM, stranda notifications@github.com wrote:

may be a version problem on ubuntu, can you try: library(devtools) install_github("christianparobek/skeleSim/skeleSim",force=T)

— Reply to this email directly or view it on GitHub https://github.com/christianparobek/skeleSim/issues/22#issuecomment-186928995 .

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/

[stranda]

yeah, for the time being you have to install on ubuntu using install_github("stranda/rmetasim")

If you want to run on windows, I can email a windows binary as well

[smhoban]

Still the same error on ubuntu with the updated rmetasim. I think it must be I'm missing something with skelesim. Is this the correct version of skelesim: install.packages("skeleSim_0.9.tar.gz")

Where in the code is the function skeleSimGUI?

On Sun, Feb 21, 2016 at 2:20 PM, stranda notifications@github.com wrote:

Hmm. Should be able to (after Install): library(skeleSim) skeleSimGUI()

Works on my linux machine, I'm installing on windows now to check

— Reply to this email directly or view it on GitHub https://github.com/christianparobek/skeleSim/issues/22#issuecomment-186894203 .

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/

[stranda]

I would definitely install the new version thats on github seems like you have an old version of skeleSim

On Mon, Feb 22, 2016 at 12:37 PM, Sean notifications@github.com wrote:

Still the same error on ubuntu with the updated rmetasim. I think it must be I'm missing something with skelesim. Is this the correct version of skelesim: install.packages("skeleSim_0.9.tar.gz")

Where in the code is the function skeleSimGUI?

On Sun, Feb 21, 2016 at 2:20 PM, stranda notifications@github.com wrote:

Hmm. Should be able to (after Install): library(skeleSim) skeleSimGUI()

Works on my linux machine, I'm installing on windows now to check

— Reply to this email directly or view it on GitHub < https://github.com/christianparobek/skeleSim/issues/22#issuecomment-186894203

.

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/

— Reply to this email directly or view it on GitHub https://github.com/christianparobek/skeleSim/issues/22#issuecomment-187283309 .

[EricArcher]

Heads-up: I'm in the middle of updating the fastsimcoal code, so it may break if you're using that simulator...

[smhoban]

skeleSimGUI() finally works on my new linux box! The GUI opens and everything is clickable. I do get the following message in R though:

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 ssClassInit: object 'analysis_funcs' not found Stack trace (innermost first): 47: ssClassInit [/home/user/R/x86_64-pc-linux-gnu-library/3.2/skeleSim/shiny/skeleSimShinyGUI/global.R#45] 46: reactiveValues 45: eval [serverInit.R#8] 44: eval 43: withVisible 42: source 41: server [/home/user/R/x86_64-pc-linux-gnu-library/3.2/skeleSim/shiny/skeleSimShinyGUI/server.R#8] 2: runApp 1: skeleSimGUI Error in ssClassInit() : object 'analysis_funcs' not found

On Mon, Feb 22, 2016 at 2:55 PM, Eric Archer notifications@github.com wrote:

Heads-up: I'm in the middle of updating the fastsimcoal code, so it may break if you're using that simulator...

— Reply to this email directly or view it on GitHub https://github.com/christianparobek/skeleSim/issues/22#issuecomment-187378688 .

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 think this is resolved