dceoy/clir repository overview

⁠clir

R Package Installer for Command Line Interface

⁠Supported versions

⁠Usage

⁠Installation or update of R packages

• Install packages via CRAN using install.packages().

  $ clir install foreach doParallel tidyverse
  

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• Install or update packages via CRAN using devtools::install_cran().

  $ clir install --devt=cran foreach doParallel tidyverse
  

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• Install or update packages via GitHub using devtools::install_github().

  $ clir install --devt=github IRkernel/IRkernel
  

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• Install or update packages via Bioconductor using BiocManager::install().

  $ clir install --bioc GenomicRanges
  

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• Install or update packages via Bioconductor using devtools::install_bioc().

  $ clir install --devt=bioc GenomicRanges
  

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• Update packages via CRAN using update.packages().

  $ clir update
  

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⁠Validation of installed R packages

• Validate loading of installed packages.

  $ clir validate foreach doParallel tidyverse
  

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⁠Session information

• Load packages and print session information.

  $ clir session foreach doParallel tidyverse
  

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Run clir --help for information.

⁠Docker image

The image is available at Docker Hub⁠.

$ docker image pull dceoy/clir

⁠Installation

⁠Installation into a local environment

1. Install R and the additional packages.

   # Ubuntu
   $ sudo apt-get -y install git libcurl4-gnutls-dev libssl-dev libxml2-dev r-base
   
   # CentOS
   $ sudo yum -y install git libcurl-devel libxml2-devel openssl-devel R-devel
   
   # Fedora
   $ sudo dnf -y install git libcurl-devel libxml2-devel openssl-devel R-devel
   
   # macOS with Homebrew
   $ brew tap homebrew/science
   $ brew install curl git openssl r
   

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2. Check out clir and run install_clir.sh.

   $ git clone https://github.com/dceoy/clir.git ~/.clir
   

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3. Install clir and the dependencies.

   $ ~/.clir/install_clir.sh
   

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   install_clir.sh installs the following R packages:

   • docopt⁠
   • yaml⁠
   • devtools⁠
   • drat⁠
   • BiocManager⁠

   clir depends on docopt and yaml, and uses devtools, drat, and BiocManager additionally if they are available.

   Run ~/.clir/install_clir.sh --help for more details of the installer.

4. Set ~/.clir/bin into ${PATH} and set ~/.clir/r/library into ${R_LIBS_USER} or ${R_LIBS}.

   $ echo 'export PATH="${HOME}/.clir/bin:${PATH}"' >> ~/.bash_profile
   $ echo 'export R_LIBS_USER="${HOME}/.clir/r/library"' >> ~/.bash_profile
   $ source ~/.bash_profile
   

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   If you use Zsh, modify ~/.zshrc instead of ~/.bash_profile.

⁠Installation into a system

Run the installer with --root if you install clir into a system. (clir is going to be installed into /usr/local then.)

$ curl -LSO https://raw.githubusercontent.com/dceoy/clir/master/install_clir.sh
$ chmod +x install_clir.sh
yy$ sudo ./install_clir.sh --root
$ rm install_clir.sh

⁠Update

⁠Update of clir in a local environment

$ ~/.clir/install_clir.sh

⁠Update of clir installed into the system

$ sudo /usr/local/src/clir/install_clir.sh --root

⁠Configuration

• Library path

  R packages are installed into a directory in ${R_LIBS_USER} nor ${R_LIBS}. If neither of them is set, a default library path is used. The default path can be checked as follows:

  $ R --slave -e '.libPaths()[1]'
  

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• CRAN and Drat repositories

  clir saves URLs of CRAN mirrors and Drat repositories into ~/.clir/r/clir.yml as a YAML file.