inst/app/README-install.md

In xhdong-umd/ctmmweb: Web App For ctmm Package

Package installation

If you met problem in the one line script, you can run these lines one by one and locate the specific problem.

You may need to restart R session and run them again when met error in package installation.

# restart R session first
remove.packages("ctmm")
if (!require("devtools")) install.packages("devtools")
devtools::install_github("rstudio/shiny")
devtools::install_github("ctmm-initiative/ctmm")

Run specific version of app

# stable version
shiny::runGitHub('ctmm-initiative/ctmm-webapp', ref = "v0.0.6")
# or latest version
shiny::runGitHub('ctmm-initiative/ctmm-webapp')

Run app in local machine without Internet

The method above always download the app before run. You can also download the app and run without Internet.

With R and dependency packages installed:

1. Download the stable version from releases page, currently v0.0.6, or the latest development version.

2. Unzip the zip to a folder, then run it with

   r if (!require("devtools")) install.packages("devtools") devtools::install_github("rstudio/shiny") devtools::install_github("ctmm-initiative/ctmm") devtools::install_github("r-lib/crayon") shiny::runApp("<absolute path to your app folder>")

Linux

• Following instructions here for installing R (assuming Ubuntu or Linux Mint). Make sure to install r-base-dev too.
• RStudio have installer for Linux.
• Some of the packages needed for the app need extra steps to install properly:

• devtools need libcurl, ssl if it's not already installed in your system. You can watch error messages to check what is required. I installed them in Linux Mint 18 with

  sudo apt-get install libcurl4-openssl-dev
  sudo apt-get install libssl-dev
  

• ctmm need rgdal, which need another two libraries in linux:

  sudo apt-get update && sudo apt-get install libgdal-dev libproj-dev
  

Known bugs

• When you start the app in RStudio, it was opened with embeded browser in RStudio, which has these known limitations:
• Windows: log scale slider not shown properly; download dialog don't prompt proper file name by default.
• Mac: download file will open a blank page, and the dowload function was executed twice so there will be two entries in report.
• Linux: download dialog do not respond.

• There is a known bug caused by data.table, openMP and mcapply in R 3.4. So it's possible to see this error when fitting models in parallel under Mac/Linux:

  r Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null. OMP: Error #13: Assertion failure at kmp_runtime.cpp(6480).

The error is pretty random and hard to reproduce, but usually you can restart R session and it should dissappear.

xhdong-umd/ctmmweb documentation built on May 29, 2019, 11:59 a.m.