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Tips for installation of MOVICS package (4/23)
 
•	Install heatmap.plus package from source code
NOTE: v1.3 is recommended
R CMD: install.packages("https://cran.r-project.org/src/contrib/Archive/heatmap.plus/heatmap.plus_1.3.tar.gz", repos = NULL, type="source")
 

•	Install SNFtool package from source code
NOTE: v2.3.0 is recommended
R CMD: install.packages("https://cran.r-project.org/src/contrib/Archive/SNFtool/SNFtool_2.3.0.tar.gz", repos = NULL, type="source")


•	How to install CIMLR with R CMD
Reference: https://github.com/danro9685/CIMLR

library("devtools")
devtools::install_github("danro9685/CIMLR", ref = 'R')
library("CIMLR")


•	Troubleshooting for installing CIMLR package
If you cannot install CIMLR package with R CMD, please try the following two solutions.

Solution 1: Update R Makevars file
In ~/.R/Makevars, add these lines.
 
FC = /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran
F77 = /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran
FLIBS = -L/opt/homebrew/Cellar/gcc/12.2.0/lib/gcc/12
 
NOTE: You can use vim to make edits to the file (https://www.linuxfoundation.org/blog/blog/classic-sysadmin-vim-101-a-beginners-guide-to-vim)
NOTE: If the ~/.R directory doesn’t exist, you create it this way: mkdir -p ~/.R
 
Solution 2: install Xcode on mac (takes ~ 30 min)
https://developer.apple.com/download/all/?q=Xcode


•	Make sure to install these packages
install.packages("BiocManager")
install.packages("devtools")
install.packages("Matrix", dependencies = TRUE)
  
 
•	GitHub access error
If you get an error like this:
 
Using github PAT from envvar GITHUB_PAT
Error: Failed to install 'unknown package' from GitHub:
  HTTP error 401.
  Bad credentials
 
  Rate limit remaining: 37/60
  Rate limit reset at: 2021-09-15 17:23:41 UTC
 
Then you need to create a personal access token (PAT) and increase your GitHub API rate limit
  - Use `usethis::browse_github_pat()` to create a Personal Access Token.
  - Use `usethis::edit_r_environ()` and add the token as `GITHUB_PAT`.
 
For example, my PAT was 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
Sys.setenv(GITHUB_PAT = "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")
 
You would do this
Sys.setenv(GITHUB_PAT = “yourPATcode”)
 
•	Install MOVICS
devtools::install_github("xlucpu/MOVICS")