"RPHAST is an R interface to the PHAST software package. It contains much of the functionality of phast within a highly-developed statistical programming environment, and is easy and fun to use."
Follow the steps below to install R, RStudio, MinGW gcc, and RPHAST onto Windows. Note: you must be an adminstrator on the Windows PC you're installing onto, and it must be connected to the internet.
1. Download and run the R installer from:
https://cran.r-project.org/bin/windows/base/R-4.2.1-win.exe.
Accept all defaults.
2. Download and run the RStudio Installer from:
https://download1.rstudio.org/desktop/windows/RStudio-2022.07.1-554.exe.
Accept all defaults.
3. Install R Tools from:
https://cran.r-project.org/bin/windows/Rtools/rtools42/files/rtools42-5253-5107-signed.exe
Accept all defaults.
4. Install the C-compiler that the RPHAST package expects: MinGW gcc from:
https://sourceforge.net/projects/mingw/files/Installer/mingw-get-setup.exe/download.
a. In your Downloads folder run 'mingw-get-setup.exe'.
b. Click 'Install', 'Continue' and 'Continue' again.
c. In the MinGW Installation Manager window, click on the checkbox next to 'mingw32-gcc-g++-bin' and select 'Mark for Installation'.
d. Select 'Apply Changes' under the Installation menu, and click the 'Apply' button, watch the installation proceed, and then click 'Close'.
45. Update the Windows Path variable to include the new GCC compiler.
a. In the Windows Search Bar next to the Start menu, type 'This PC'
b. In the entry that appears, click on 'Properties'
c. Click on 'Advanced System Settings'
d. Click on 'Environment Varialbles'
e. In the lower box, 'System Variables', scroll down to the variable labelled 'Path', and double-click on that entry to open it's editing window.
f. In the editing window, click the 'New' button, and type 'c:\mingw\bin' and click 'OK'.
56. Open RStudio, and install the devtools package:
a. Under Tools menu, select 'Install Packages'
b. In the Install Packages window, under 'Packages', enter 'devtools'.
c. Click 'Install'
d. Watch the installation progress in console window.
67. Install RPHAST using the devtools command in RStudio.
devtools::install_github("CshlSiepelLab/RPHAST
R will ask to install R Tools, an add-on package. Accept the offer.
After a pause, R will download the package, and Windows will ask for administrative permission to be allowed to install it. Let it. Wait patiently while R-Tools installs.
After R Tools finishes installing, Quit your RStudio session, log back in, and run the devtools command again. (Up arrow should retrieve it).
The installation will proceed in the console, and should end without errors.
