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")