- ================== Welcome to rPkgsInstall ==================
- Install/update/remove R packages for AFNI
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Version 0.0.1, Nov 3, 2014 Author: Gang Chen (gangchen@mail.nih.gov) Website - http://afni.nimh.nih.gov/sscc/gangc SSCC/NIMH, National Institutes of Health, Bethesda MD 20892 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
rPkgsInstall is a program for installing, checking, updating, or removing any R packages. It conveniently runs on the shell terminal instead of the R prompt. Check out the examples below or the option specifications for usage details.
rPkgsInstall -pkgs ALL
rPkgsInstall -pkgs ALL -site ‘http://cran.case.edu/‘
rPkgsInstall -pkgs ‘afex,phia,paran’ rPkgsInstall -pkgs ‘snow,nlme,psych’ -site ‘http://cran.revolutionanalytics.com‘
rPkgsInstall -pkgs ALL -update rPkgsInstall -pkgs ALL -remove
rPkgsInstall -pkgs ALL -update -site ‘http://cran.fhcrc.org/‘ rPkgsInstall -pkgs ‘lme4,pixmap,plotrix’ -check rPkgsInstall -pkgs ‘afex,phia,paran’ -update rPkgsInstall -pkgs ‘boot’ -remove rPkgsInstall -pkgs ‘snow,nlme,vars’ -update -site ‘http://cran.cs.wwu.edu/‘
- -check\ : This option verifies whether all or the user-specified R packages
- listed in option -pkgs are installed on the computer, but it does not install/update/remove the packages.
-help: this help message
- -pkgs package_list: List all the packages that you would like to install,
- update or move. This option is required for installation, update,
or removal. The absence of both options -update and -remove means installation. The package names should be separated with comma (,) without any other characters such as spaces, and should be surrounded within single/double quotes. For example, -pkgs “afex,phia”. If package_list is set as ALL, all the following packages required for AFNI programs will be installed, updated, or removed:
‘afex’, ‘phia’, ‘snow’, ‘nlme’, ‘lme4’, ‘paran’, ‘psych’.
You can use rPkgsInstall to install, update, or remove any R packages, and they do not have to be in the list above.
- -remove: This option indicates that all or the user-specified R packages in AFNI
- will be purged from your computer. The absence of the option (default) means installing or updating, but no removing.
-show_allowed_options: list of allowed options
- -site download_website: You can specify the package repository website within
single/double quotes. The current sites can be found at
http://cran.r-project.org/mirrors.html
The default is ‘http://cran.mtu.edu/‘ at Michigan Technological University, Houghton, MI.
- -update: This option indicates that all or the user-specified R packages in AFNI
will be updated. The absence of the option (default) means no updating. A package specified in ‘-pkgs package_list’ that has not been installed on the computer will be installed under this option. WARNING: Updating some R packages may require that R be ugraded to the
most recent version.