MacOS

Install R #

Following the instructions in the installing pages of MacOS to install R: https://cran.r-project.org/

Install dependences for system #

MCnebula2 requires the R package ChemmineOB for visualizing chemical structures. In our debugging, ChemmineOB needs to be pre-installed on MacOS with ‘Open Babel’ so that it can be used.

(Option) Install Open Babel via ‘Homebrew’ #

Please check the official website for detailed guidelines about installation: https://github.com/Homebrew/install. The following is the copied command for installing that:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

For Chinese people, the following command can be used if there is some trouble in network connection:

/bin/bash -c "$(curl -fsSL https://gitee.com/cunkai/HomebrewCN/raw/master/Homebrew.sh)"

After the ‘Homebrew’ has been installed, restart the terminal, and then:

## config the github first, so that the `git` can be run successfully.
git config --global --add safe.directory /opt/homebrew/Library/Taps/homebrew/homebrew-core
git config --global --add safe.directory /opt/homebrew/Library/Taps/homebrew/homebrew-cask
brew install open-babel

(Option) Other methods #

See http://openbabel.org/wiki/Main_Page for guidelines.

Install R packages from ‘Bioconductor’ #

Installing R packages from Bioconductor:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c("BiocStyle", "ChemmineOB"))

Install MCnebula2 from github #

Use devtools or remotes to install MCnebula2:

if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")
remotes::install_github("Cao-lab-zcmu/MCnebula2")

(Option) Install exMCnebula2 from github #

Please refer to The instructions of Linux. Click here