asgr / ss19b-robotham

SS19B-Robotham

Use R version 3.5.1 as a minimum

First time install, build, and run

On MacOS assuming R (>=3.5.0) is already installed

• Build straight from repo using: ./run_Build_from_scratch.sh
• Run the example: ./run_example1_non_interactive.sh
• To run the example interactively: Cut and paste the following into an R session (started with command R, ended with CTRL D)

On OzSTAR assuming R 3.5.1 is available as a module

• module load r/3.5.1
• From R run install.packages("devtools") and say you want a private library when it asks
• From R run install.packages("BiocManager")
• From R run BiocManager::install("EBImage")
• ./run_Build_from_scratch.sh
• ./run_example1_non_interactive.sh

On Windows using R version 3.6.x:

From R session (or from RStudio console) -

• install.packages("devtools")
• install.packages("provis")
• install.packages("akima")
• install.packages("imager")
• install.packages("BiocManager")
• BiocManager::install("EBIMage")
• library(devtools)
• install_github("asgr/magicaxis")
• install_github("asgr/Profound")

To run an example:

library(ProFound)
image=readFITS(system.file("extdata", 'VIKING/mystery_VIKING_Z.fits', package="ProFound"))
profound=profoundProFound(image, skycut=1.5, magzero=30, verbose=TRUE, plot=TRUE)

Building from cloned repo

Something like this (not sure of the minimum steps):

On MacOS assuming RStudio is already installed

1. Launch RStudio
2. Use File/Open Project... and navigate to the "ProFound" sub directory of the repo clone
3. If required, "Build/Configure Build Tools..." and under "Build Tools" select "Package" for "Project build tools" ...
4. Select "Use devtools package if available" and OK
5. To build select "Build/Clean and Rebuild"