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christianparobek / skeleSim

Null models, performance testing, and power estimation with population simulations
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strataG new version required to build skeleSim #18

Closed stranda closed 8 years ago

stranda commented 8 years ago

I found that I had to clone strataG from Eric's github repository and build locally to make sure that skeleSim would build. The current CRAN version does not export something...

christianparobek commented 8 years ago

Here's the link: https://github.com/EricArcher/strataG

This dev version will require installation of some dependencies. One of the dependencies, apex, depends on phangorn, which depends on Biostrings which is on Bioconductor - not CRAN.

MichelleDBG commented 8 years ago

I am trying to run a simulation to produce a skeleSim object to test in the analysis_funcs. I get Fastsimcoal and set some parameters. It is now giving me the looping error: "Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' "

I installed phangorn, apex, and Biostrings following the Bioconductor instructions. Any ideas what I've got wrong with BioGenerics?

christianparobek commented 8 years ago

I get that same message as well...

smhoban commented 8 years ago

Did this get resolved?

smhoban commented 8 years ago

On windows I still get an error with 'dplyr'. Just FYI. I'll try on ubuntu

\ preparing package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called 'dplyr' Error : package 'apex' could not be loaded ERROR: lazy loading failed for package 'strataG'

bjcochrane commented 8 years ago

Check your R version. If it's 3.11 or less dplyr won't load and the error results.

Sent from my iPhone

On Feb 16, 2016, at 2:13 PM, Sean notifications@github.com wrote:

On windows I still get an error with 'dplyr'. Just FYI. I'll try on ubuntu

\ preparing package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called 'dplyr' Error : package 'apex' could not be loaded ERROR: lazy loading failed for package 'strataG'

removing 'C:/Users/seanmh/Documents/R/win-library/3.2/strataG' restoring previous 'C:/Users/seanmh/Documents/R/win-library/3.2/strataG' Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) : problem copying C:\Users\seanmh\Documents\R\win-library\3.2\00LOCK-strataG\strataG\libs\i386\strataG.dll to C:\Users\seanmh\Documents\R\win-library\3.2\strataG\libs\i386\strataG.dll: Permission denied Error: Command failed (1) — Reply to this email directly or view it on GitHub.

smhoban commented 8 years ago

Thanks Bruce! Will do.

On Tue, Feb 16, 2016 at 3:20 PM, Bruce Cochrane notifications@github.com wrote:

Check your R version. If it's 3.11 or less dplyr won't load and the error results.

Sent from my iPhone

On Feb 16, 2016, at 2:13 PM, Sean notifications@github.com wrote:

On windows I still get an error with 'dplyr'. Just FYI. I'll try on ubuntu

\ preparing package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called 'dplyr' Error : package 'apex' could not be loaded ERROR: lazy loading failed for package 'strataG'

removing 'C:/Users/seanmh/Documents/R/win-library/3.2/strataG' restoring previous 'C:/Users/seanmh/Documents/R/win-library/3.2/strataG' Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) : problem copying C:\Users\seanmh\Documents\R\win-library\3.2\00LOCK-strataG\strataG\libs\i386\strataG.dll to C:\Users\seanmh\Documents\R\win-library\3.2\strataG\libs\i386\strataG.dll: Permission denied Error: Command failed (1)

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/christianparobek/skeleSim/issues/18#issuecomment-184861284 .

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 commented 8 years ago

I think this is resolved